9QQB | pdb_00009qqb

Quaternary complex of a translating ribosome, NAC, NMT1, and NatA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of cotranslational protein N-myristoylation in human cells.

Gamerdinger, M.Echeverria, B.Lentzsch, A.M.Burg, N.Fan, Z.Jaskolowski, M.Scaiola, A.Piening, S.Shan, S.O.Ban, N.Deuerling, E.

(2025) Mol Cell 85: 2749

  • DOI: https://doi.org/10.1016/j.molcel.2025.06.015
  • Primary Citation of Related Structures:  
    9QQA, 9QQB

  • PubMed Abstract: 

    N-myristoyltransferases (NMTs) cotranslationally transfer the fatty acid myristic acid to the N terminus of newly synthesized proteins, regulating their function and cellular localization. These enzymes are important drug targets for the treatment of cancer and viral infections. N-myristoylation of nascent proteins occurs specifically on N-terminal glycine residues after the excision of the initiator methionine by methionine aminopeptidases (METAPs). How NMTs interact with ribosomes and gain timely and specific access to their substrates remains unknown. Here, we show that human NMT1 exchanges with METAP1 at the ribosomal tunnel exit to form an active cotranslational complex together with the nascent polypeptide-associated complex (NAC). NMT1 binding is sequence selective and specifically triggered by methionine excision, which exposes the N-myristoylation motif in the nascent chain. The revealed mode of interaction of NMT1 with NAC and the methionine-cleaved nascent protein elucidates how a specific subset of proteins can be efficiently N-myristoylated in human cells.


  • Organizational Affiliation
    • Department of Biology, Molecular Microbiology, University of Konstanz, 78457 Konstanz, Germany. Electronic address: martin.gamerdinger@uni-konstanz.de.

Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2D [auth BA]257Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3E [auth BB]403Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4F [auth BC]413Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18G [auth BD]297Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6H [auth BE]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal Protein uL30I [auth BF]247Oryctolagus cuniculusMutation(s): 4 
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Find proteins for G1TUB1 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aJ [auth BG]266Oryctolagus cuniculusMutation(s): 0 
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PHAROS:  P62424
GTEx:  ENSG00000148303 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9K [auth BH]192Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10L [auth BI]214Oryctolagus cuniculusMutation(s): 0 
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Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11M [auth BJ]178Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainN [auth BK]12Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13O [auth BL]211Oryctolagus cuniculusMutation(s): 2 
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Find proteins for G1TKB3 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14P [auth BM]218Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth BN]204Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13R [auth BO]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22S [auth BP]184Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL18T [auth BQ]188Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for F6QKI9 (Callithrix jacchus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19U [auth BR]196Oryctolagus cuniculusMutation(s): 3 
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Find proteins for G1TJR3 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20V [auth BS]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21W [auth BT]160Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22X [auth BU]128Oryctolagus cuniculusMutation(s): 5 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23Y [auth BV]140Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24Z [auth BW]157Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23AA [auth BX]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26BA [auth BY]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27CA [auth BZ]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aDA [auth Ba]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EA [auth Bb]245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30FA [auth Bc]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31GA [auth Bd]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32HA [auth Be]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0AAA9WVN6 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aIA [auth Bf]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34JA [auth Bg]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35KA [auth Bh]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36LA [auth Bi]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37MA [auth Bj]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38NA [auth Bk]70Oryctolagus cuniculusMutation(s): 1 
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Find proteins for G1U001 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39-likeOA [auth Bl]51Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eL40 fusion proteinPA [auth Bm]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P0DXC2 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42QA [auth Bo]106Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0AAA9WX15 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aRA [auth Bp]92Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
[histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5BSA [auth Br]137Oryctolagus cuniculusMutation(s): 1 
EC: 2.1.1.361 (PDB Primary Data), 2.1.1.362 (PDB Primary Data)
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Find proteins for A0A8C0DF35 (Balaenoptera musculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10TA [auth Bs]318Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SPK4 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12UA [auth Bt]165Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL1VA [auth Bv]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent polypeptide-associated complex subunit alphaWA [auth Nt]215Homo sapiensMutation(s): 0 
Gene Names: NACAHSD48
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GTEx:  ENSG00000196531 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Transcription factor BTF3XA [auth Nu]162Homo sapiensMutation(s): 0 
Gene Names: BTF3NACBOK/SW-cl.8
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GTEx:  ENSG00000145741 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 15, NatA auxiliary subunitYA [auth XA]866Homo sapiensMutation(s): 0 
Gene Names: NAA15GA19NARG1NATHTBDN100
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GTEx:  ENSG00000164134 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 10ZA [auth XB]235Homo sapiensMutation(s): 0 
Gene Names: NAA10ARD1ARD1ATE2
EC: 2.3.1.255
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GTEx:  ENSG00000102030 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase 1AB [auth MA]496Homo sapiensMutation(s): 0 
Gene Names: NMT1NMT
EC: 2.3.1.97 (PDB Primary Data), 2.3.1 (PDB Primary Data)
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GTEx:  ENSG00000136448 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27CB [auth AA]84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28DB [auth AB]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eS31 fusion proteinEB [auth AC]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like FUBI-ribosomal protein eS30 fusion proteinFB [auth AD]133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
eS26GB [auth AE]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1HB [auth AF]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14IB [auth AG]56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2KB [auth AZ]295Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aLB [auth Aa]264Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2MB [auth Ab]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3NB [auth Ac]281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4OB [auth Ad]263Oryctolagus cuniculusMutation(s): 4 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7PB [auth Ae]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6QB [auth Af]249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7RB [auth Ag]432Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8SB [auth Ah]208Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4TB [auth Ai]194Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
S10_plectin domain-containing proteinUB [auth Aj]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17VB [auth Ak]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS12WB [auth Al]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15XB [auth Am]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11YB [auth An]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19ZB [auth Ao]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9AC [auth Ap]172Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17BC [auth Aq]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13CC [auth Ar]152Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19DC [auth As]145Oryctolagus cuniculusMutation(s): 2 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10EC [auth At]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21FC [auth Au]84Oryctolagus cuniculusMutation(s): 1 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8GC [auth Av]130Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23HC [auth Aw]143Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24IC [auth Ax]130Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25JC [auth Ay]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS32KC [auth Az]25Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S rRNAA [auth B5]4,808Oryctolagus cuniculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNAB [auth B7]120Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S rRNAC [auth B8]158Oryctolagus cuniculus
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Entity ID: 54
MoleculeChains LengthOrganismImage
18S rRNABB [auth A2]1,870Oryctolagus cuniculus
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Entity ID: 62
MoleculeChains LengthOrganismImage
P site Phe tRNAJB [auth AT]76Oryctolagus cuniculus
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
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MU [auth XA]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
SPM
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VC [auth B5],
VU [auth A2],
YC [auth B5]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
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AD [auth B5]
BD [auth B5]
CD [auth B5]
DD [auth B5]
ED [auth B5]
AD [auth B5],
BD [auth B5],
CD [auth B5],
DD [auth B5],
ED [auth B5],
FD [auth B5],
GD [auth B5],
HD [auth B5],
LC [auth B5],
MC [auth B5],
NC [auth B5],
NU [auth A2],
OC [auth B5],
OU [auth A2],
PC [auth B5],
PU [auth A2],
QC [auth B5],
QU [auth A2],
RC [auth B5],
RU [auth A2],
SC [auth B5],
SU [auth A2],
TC [auth B5],
TU [auth A2],
UC [auth B5],
UU [auth A2],
WC [auth B5],
WT [auth BS],
XC [auth B5],
ZC [auth B5]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DAA [auth AC]
EAA [auth AE]
EU [auth Bg]
FAA [auth AG]
GU [auth Bj]
DAA [auth AC],
EAA [auth AE],
EU [auth Bg],
FAA [auth AG],
GU [auth Bj],
IU [auth Bm],
JU [auth Bo],
LU [auth Bp]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth B5]
AF [auth B5]
AG [auth B5]
AH [auth B5]
AI [auth B5]
AE [auth B5],
AF [auth B5],
AG [auth B5],
AH [auth B5],
AI [auth B5],
AJ [auth B5],
AK [auth B5],
AL [auth B5],
AM [auth B5],
AN [auth B5],
AT [auth B8],
AU [auth Ba],
AV [auth A2],
AW [auth A2],
AX [auth A2],
AY [auth A2],
BAA [auth A2],
BE [auth B5],
BF [auth B5],
BG [auth B5],
BH [auth B5],
BI [auth B5],
BJ [auth B5],
BK [auth B5],
BL [auth B5],
BM [auth B5],
BN [auth B5],
BT [auth B8],
BV [auth A2],
BW [auth A2],
BX [auth A2],
BY [auth A2],
CE [auth B5],
CF [auth B5],
CG [auth B5],
CH [auth B5],
CI [auth B5],
CJ [auth B5],
CK [auth B5],
CL [auth B5],
CM [auth B5],
CN [auth B5],
CT [auth B8],
CV [auth A2],
CW [auth A2],
CX [auth A2],
CY [auth A2],
DE [auth B5],
DF [auth B5],
DG [auth B5],
DH [auth B5],
DI [auth B5],
DJ [auth B5],
DK [auth B5],
DL [auth B5],
DM [auth B5],
DN [auth B5],
DT [auth B8],
DV [auth A2],
DW [auth A2],
DX [auth A2],
DY [auth A2],
EE [auth B5],
EF [auth B5],
EG [auth B5],
EH [auth B5],
EI [auth B5],
EJ [auth B5],
EK [auth B5],
EL [auth B5],
EM [auth B5],
EN [auth B5],
ET [auth B8],
EV [auth A2],
EW [auth A2],
EX [auth A2],
EY [auth A2],
FE [auth B5],
FF [auth B5],
FG [auth B5],
FH [auth B5],
FI [auth B5],
FJ [auth B5],
FK [auth B5],
FL [auth B5],
FM [auth B5],
FN [auth B5],
FT [auth B8],
FV [auth A2],
FW [auth A2],
FX [auth A2],
FY [auth A2],
GE [auth B5],
GF [auth B5],
GG [auth B5],
GH [auth B5],
GI [auth B5],
GJ [auth B5],
GK [auth B5],
GL [auth B5],
GM [auth B5],
GN [auth B5],
GT [auth B8],
GV [auth A2],
GW [auth A2],
GX [auth A2],
GY [auth A2],
HE [auth B5],
HF [auth B5],
HG [auth B5],
HH [auth B5],
HI [auth B5],
HJ [auth B5],
HK [auth B5],
HL [auth B5],
HM [auth B5],
HN [auth B5],
HT [auth B8],
HU [auth Bj],
HV [auth A2],
HW [auth A2],
HX [auth A2],
HY [auth A2],
IAA [auth Aw],
ID [auth B5],
IE [auth B5],
IF [auth B5],
IG [auth B5],
IH [auth B5],
II [auth B5],
IJ [auth B5],
IK [auth B5],
IL [auth B5],
IM [auth B5],
IN [auth B5],
IV [auth A2],
IW [auth A2],
IX [auth A2],
IY [auth A2],
JD [auth B5],
JE [auth B5],
JF [auth B5],
JG [auth B5],
JH [auth B5],
JI [auth B5],
JJ [auth B5],
JK [auth B5],
JL [auth B5],
JM [auth B5],
JN [auth B5],
JS [auth B5],
JV [auth A2],
JW [auth A2],
JX [auth A2],
JY [auth A2],
KD [auth B5],
KE [auth B5],
KF [auth B5],
KG [auth B5],
KH [auth B5],
KI [auth B5],
KJ [auth B5],
KK [auth B5],
KL [auth B5],
KM [auth B5],
KN [auth B5],
KS [auth B5],
KV [auth A2],
KW [auth A2],
KX [auth A2],
KY [auth A2],
LD [auth B5],
LE [auth B5],
LF [auth B5],
LG [auth B5],
LH [auth B5],
LI [auth B5],
LJ [auth B5],
LK [auth B5],
LL [auth B5],
LM [auth B5],
LN [auth B5],
LV [auth A2],
LW [auth A2],
LX [auth A2],
LY [auth A2],
MD [auth B5],
ME [auth B5],
MF [auth B5],
MG [auth B5],
MH [auth B5],
MI [auth B5],
MJ [auth B5],
MK [auth B5],
ML [auth B5],
MM [auth B5],
MN [auth B5],
MV [auth A2],
MW [auth A2],
MX [auth A2],
MY [auth A2],
ND [auth B5],
NE [auth B5],
NF [auth B5],
NG [auth B5],
NH [auth B5],
NI [auth B5],
NJ [auth B5],
NK [auth B5],
NL [auth B5],
NM [auth B5],
NN [auth B5],
NS [auth B7],
NV [auth A2],
NW [auth A2],
NX [auth A2],
NY [auth A2],
OD [auth B5],
OE [auth B5],
OF [auth B5],
OG [auth B5],
OH [auth B5],
OI [auth B5],
OJ [auth B5],
OK [auth B5],
OL [auth B5],
OM [auth B5],
ON [auth B5],
OS [auth B7],
OT [auth BB],
OV [auth A2],
OW [auth A2],
OX [auth A2],
OY [auth A2],
PD [auth B5],
PE [auth B5],
PF [auth B5],
PG [auth B5],
PH [auth B5],
PI [auth B5],
PJ [auth B5],
PK [auth B5],
PL [auth B5],
PM [auth B5],
PN [auth B5],
PS [auth B7],
PT [auth BB],
PV [auth A2],
PW [auth A2],
PX [auth A2],
PY [auth A2],
QD [auth B5],
QE [auth B5],
QF [auth B5],
QG [auth B5],
QH [auth B5],
QI [auth B5],
QJ [auth B5],
QK [auth B5],
QL [auth B5],
QM [auth B5],
QN [auth B5],
QS [auth B7],
QV [auth A2],
QW [auth A2],
QX [auth A2],
QY [auth A2],
RD [auth B5],
RE [auth B5],
RF [auth B5],
RG [auth B5],
RH [auth B5],
RI [auth B5],
RJ [auth B5],
RK [auth B5],
RL [auth B5],
RM [auth B5],
RN [auth B5],
RS [auth B7],
RV [auth A2],
RW [auth A2],
RX [auth A2],
RY [auth A2],
SD [auth B5],
SE [auth B5],
SF [auth B5],
SG [auth B5],
SH [auth B5],
SI [auth B5],
SJ [auth B5],
SK [auth B5],
SL [auth B5],
SM [auth B5],
SN [auth B5],
SS [auth B7],
ST [auth BP],
SV [auth A2],
SW [auth A2],
SX [auth A2],
SY [auth A2],
TD [auth B5],
TE [auth B5],
TF [auth B5],
TG [auth B5],
TH [auth B5],
TI [auth B5],
TJ [auth B5],
TK [auth B5],
TL [auth B5],
TM [auth B5],
TN [auth B5],
TS [auth B7],
TV [auth A2],
TW [auth A2],
TX [auth A2],
TY [auth A2],
UD [auth B5],
UE [auth B5],
UF [auth B5],
UG [auth B5],
UH [auth B5],
UI [auth B5],
UJ [auth B5],
UK [auth B5],
UL [auth B5],
UM [auth B5],
UN [auth B5],
US [auth B7],
UV [auth A2],
UW [auth A2],
UX [auth A2],
UY [auth A2],
VD [auth B5],
VE [auth B5],
VF [auth B5],
VG [auth B5],
VH [auth B5],
VI [auth B5],
VJ [auth B5],
VK [auth B5],
VL [auth B5],
VM [auth B5],
VN [auth B5],
VS [auth B7],
VT [auth BR],
VV [auth A2],
VW [auth A2],
VX [auth A2],
VY [auth A2],
WD [auth B5],
WE [auth B5],
WF [auth B5],
WG [auth B5],
WH [auth B5],
WI [auth B5],
WJ [auth B5],
WK [auth B5],
WL [auth B5],
WM [auth B5],
WN [auth B5],
WU [auth A2],
WV [auth A2],
WW [auth A2],
WX [auth A2],
WY [auth A2],
XD [auth B5],
XE [auth B5],
XF [auth B5],
XG [auth B5],
XH [auth B5],
XI [auth B5],
XJ [auth B5],
XK [auth B5],
XL [auth B5],
XM [auth B5],
XN [auth B5],
XU [auth A2],
XV [auth A2],
XW [auth A2],
XX [auth A2],
XY [auth A2],
YD [auth B5],
YE [auth B5],
YF [auth B5],
YG [auth B5],
YH [auth B5],
YI [auth B5],
YJ [auth B5],
YK [auth B5],
YL [auth B5],
YM [auth B5],
YT [auth BV],
YU [auth A2],
YV [auth A2],
YW [auth A2],
YX [auth A2],
YY [auth A2],
ZD [auth B5],
ZE [auth B5],
ZF [auth B5],
ZG [auth B5],
ZH [auth B5],
ZI [auth B5],
ZJ [auth B5],
ZK [auth B5],
ZL [auth B5],
ZM [auth B5],
ZS [auth B8],
ZU [auth A2],
ZV [auth A2],
ZW [auth A2],
ZX [auth A2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AAA [auth A2]
AO [auth B5]
AP [auth B5]
AQ [auth B5]
AR [auth B5]
AAA [auth A2],
AO [auth B5],
AP [auth B5],
AQ [auth B5],
AR [auth B5],
AS [auth B5],
AZ [auth A2],
BO [auth B5],
BP [auth B5],
BQ [auth B5],
BR [auth B5],
BS [auth B5],
BU [auth Bb],
BZ [auth A2],
CAA [auth A2],
CO [auth B5],
CP [auth B5],
CQ [auth B5],
CR [auth B5],
CS [auth B5],
CU [auth Bb],
CZ [auth A2],
DO [auth B5],
DP [auth B5],
DQ [auth B5],
DR [auth B5],
DS [auth B5],
DU [auth Be],
DZ [auth A2],
EO [auth B5],
EP [auth B5],
EQ [auth B5],
ER [auth B5],
ES [auth B5],
EZ [auth A2],
FO [auth B5],
FP [auth B5],
FQ [auth B5],
FR [auth B5],
FS [auth B5],
FU [auth Bj],
FZ [auth A2],
GAA [auth Ad],
GO [auth B5],
GP [auth B5],
GQ [auth B5],
GR [auth B5],
GS [auth B5],
GZ [auth A2],
HAA [auth Ar],
HO [auth B5],
HP [auth B5],
HQ [auth B5],
HR [auth B5],
HS [auth B5],
HZ [auth A2],
IO [auth B5],
IP [auth B5],
IQ [auth B5],
IR [auth B5],
IS [auth B5],
IT [auth B8],
IZ [auth A2],
JO [auth B5],
JP [auth B5],
JQ [auth B5],
JR [auth B5],
JT [auth B8],
JZ [auth A2],
KO [auth B5],
KP [auth B5],
KQ [auth B5],
KR [auth B5],
KT [auth B8],
KU [auth Bo],
KZ [auth A2],
LO [auth B5],
LP [auth B5],
LQ [auth B5],
LR [auth B5],
LS [auth B5],
LT [auth B8],
LZ [auth A2],
MO [auth B5],
MP [auth B5],
MQ [auth B5],
MR [auth B5],
MS [auth B5],
MT [auth B8],
MZ [auth A2],
NO [auth B5],
NP [auth B5],
NQ [auth B5],
NR [auth B5],
NT [auth BA],
NZ [auth A2],
OO [auth B5],
OP [auth B5],
OQ [auth B5],
OR [auth B5],
OZ [auth A2],
PO [auth B5],
PP [auth B5],
PQ [auth B5],
PR [auth B5],
PZ [auth A2],
QO [auth B5],
QP [auth B5],
QQ [auth B5],
QR [auth B5],
QT [auth BI],
QZ [auth A2],
RO [auth B5],
RP [auth B5],
RQ [auth B5],
RR [auth B5],
RT [auth BN],
RZ [auth A2],
SO [auth B5],
SP [auth B5],
SQ [auth B5],
SR [auth B5],
SZ [auth A2],
TO [auth B5],
TP [auth B5],
TQ [auth B5],
TR [auth B5],
TT [auth BQ],
TZ [auth A2],
UO [auth B5],
UP [auth B5],
UQ [auth B5],
UR [auth B5],
UT [auth BQ],
UZ [auth A2],
VO [auth B5],
VP [auth B5],
VQ [auth B5],
VR [auth B5],
VZ [auth A2],
WO [auth B5],
WP [auth B5],
WQ [auth B5],
WR [auth B5],
WS [auth B7],
WZ [auth A2],
XO [auth B5],
XP [auth B5],
XQ [auth B5],
XR [auth B5],
XS [auth B7],
XT [auth BT],
XZ [auth A2],
YN [auth B5],
YO [auth B5],
YP [auth B5],
YQ [auth B5],
YR [auth B5],
YS [auth B7],
YZ [auth A2],
ZN [auth B5],
ZO [auth B5],
ZP [auth B5],
ZQ [auth B5],
ZR [auth B5],
ZT [auth BY],
ZY [auth A2],
ZZ [auth A2]
UNKNOWN ATOM OR ION
X
Modified Residues  6 Unique
IDChains TypeFormula2D DiagramParent
V5N
Query on V5N
D [auth BA]L-PEPTIDE LINKINGC6 H9 N3 O3HIS
HIC
Query on HIC
E [auth BB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
MLZ
Query on MLZ
EA [auth Bb]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
M3L
Query on M3L
PA [auth Bm]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
NMM
Query on NMM
DC [auth As]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
HY3
Query on HY3
HC [auth Aw]L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_212308
Swiss National Science Foundation51NF40-205601
European Research Council (ERC)European Union101072047

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-30
    Changes: Data collection, Database references