7O5B | pdb_00007o5b

Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP bound

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 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

Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp.

Czech, L., Mais, C.N., Kratzat, H., Sarmah, P., Giammarinaro, P., Freibert, S.A., Esser, H.F., Musial, J., Berninghausen, O., Steinchen, W., Beckmann, R., Koch, H.G., Bange, G.

(2022) Nat Commun 13: 1069-1069

  • DOI: https://doi.org/10.1038/s41467-022-28675-0
  • Primary Citation of Related Structures:  
    7O5B, 7O9F, 7O9G, 7O9H, 7O9I

  • PubMed Abstract: 

    The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli.

    • Organizational Affiliation: 
    • Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry Philipps-Universität Marburg, Marburg, Germany. laura.czech@staff.uni-marburg.de.

Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle proteinD [auth g]447Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ffh, BSU15980
EC: 3.6.5.4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MifM-stalling constructE [auth h]96Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10F [auth p]166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11G [auth q]141Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2J [auth Z]277Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3K [auth a]208Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4L [auth b]207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5M [auth c]179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6N [auth d]179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13O [auth e]145Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14P [auth f]122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15Q [auth i]146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16R [auth j]144Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17S [auth k]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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50S ribosomal protein L18T [auth l]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19U [auth m]115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20V [auth n]119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21W [auth o]102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L22X [auth r]113Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Y [auth s]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth t]103Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AA [auth u]94Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BA [auth v]62Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CA [auth w]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DA [auth x]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32EA [auth 0]59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1FA [auth 1]49Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34GA [auth 2]44Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35HA [auth 3]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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50S ribosomal protein L36IA [auth 4]37Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31JA [auth 6]66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2LA [auth B]246Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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30S ribosomal protein S3MA [auth C]218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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30S ribosomal protein S4NA [auth D]200Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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30S ribosomal protein S5OA [auth E]166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6PA [auth F]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7QA [auth G]156Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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30S ribosomal protein S8RA [auth H]132Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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30S ribosomal protein S9SA [auth I]130Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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30S ribosomal protein S10TA [auth J]102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11UA [auth K]131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12VA [auth L]138Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13WA [auth M]121Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14XA [auth N]61Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15YA [auth O]89Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for P21473 (Bacillus subtilis (strain 168))
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UniProt GroupP21473
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16ZA [auth P]90Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17AB [auth Q]87Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for P12874 (Bacillus subtilis (strain 168))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18BB [auth R]79Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19CB [auth S]92Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20DB [auth T]88Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
tRNAA [auth U]77Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 2
MoleculeChains LengthOrganismImage
mRNAB [auth V]8Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 3
MoleculeChains LengthOrganismImage
SRP RNA (266-MER)C [auth W]266Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 8
MoleculeChains LengthOrganismImage
23S rRNA (2887-MER)H [auth X]2,887Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S rRNA (112-MER)I [auth Y]112Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 37
MoleculeChains LengthOrganismImage
16S rRNA (1533-MER)KA [auth A]1,533Bacillus subtilis subsp. subtilis str. 168
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G4P
Query on G4P
Download Ideal Coordinates CCD File 
EB [auth g]GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyTRR174

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary