9Q87 | pdb_00009q87

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+

• PDB DOI: https://doi.org/10.2210/pdb9Q87/pdb
• EM Map EMD-15793: EMDB EMDataResource
• NAKB: 9Q87

• Classification: RIBOSOME
• Organism(s): Escherichia coli B
• Mutation(s): No 


• Deposited: 2025-02-23 Released: 2025-05-14 
• Deposition Author(s): Leonarski, f., Henning-Knechtel, A., Kirmizialtin, S., Ennifar, E., Auffinger, P.
• Funding Organization(s): Centre National de la Recherche Scientifique (CNRS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8B0X

Literature

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angs. resolution bacterial ribosome structure - Part I: Mg2+.

Leonarski, F., Henning-Knechtel, A., Kirmizialtin, S., Ennifar, E., Auffinger, P.

(2024) Nucleic Acids Res 

• DOI: https://doi.org/10.1093/nar/gkae1235

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 49-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 49-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,198.12 kDa 
• Atom Count: 166,856 
• Modeled Residue Count: 10,418 
• Deposited Residue Count: 10,643 
• Unique protein chains: 49
• Unique nucleic acid chains: 6

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS2	B	233	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Explore P0A7V0  Go to UniProtKB:  P0A7V0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS3	C	233	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Explore P0A7V3  Go to UniProtKB:  P0A7V3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS4	D	206	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Explore P0A7V8  Go to UniProtKB:  P0A7V8

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS5	E	167	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Explore P0A7W1  Go to UniProtKB:  P0A7W1

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS6, fully modified isoform	F	135	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358  Go to UniProtKB:  P02358

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS7	G	179	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P02359 (Escherichia coli (strain K12)) Explore P02359  Go to UniProtKB:  P02359

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS8	H	130	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7  Go to UniProtKB:  P0A7W7

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS9	I	130	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Explore P0A7X3  Go to UniProtKB:  P0A7X3

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS10	J	103	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Explore P0A7R5  Go to UniProtKB:  P0A7R5

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS11	K	129	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Explore P0A7R9  Go to UniProtKB:  P0A7R9

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS12	L	124	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Explore P0A7S3  Go to UniProtKB:  P0A7S3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS13	M	118	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Explore P0A7S9  Go to UniProtKB:  P0A7S9

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS14	N	101	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12)) Explore P0AG59  Go to UniProtKB:  P0AG59

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS15	O	89	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12)) Explore P0ADZ4  Go to UniProtKB:  P0ADZ4

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS16	P	82	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Explore P0A7T3  Go to UniProtKB:  P0A7T3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS17	Q	84	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12)) Explore P0AG63  Go to UniProtKB:  P0AG63

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS18	R	75	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7  Go to UniProtKB:  P0A7T7

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS19	S	92	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Explore P0A7U3  Go to UniProtKB:  P0A7U3

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS20	T	87	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7  Go to UniProtKB:  P0A7U7

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS21	U	71	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P68679 (Escherichia coli (strain K12)) Explore P68679  Go to UniProtKB:  P68679

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL33	X [auth 0]	55	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Explore P0A7N9  Go to UniProtKB:  P0A7N9

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL34	Y [auth 1]	46	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5  Go to UniProtKB:  P0A7P5

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL35	Z [auth 2]	65	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1  Go to UniProtKB:  P0A7Q1

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL36	AA [auth 3]	38	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Explore P0A7Q6  Go to UniProtKB:  P0A7Q6

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL11	BA [auth 5]	141	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12)) Explore P0A7J7  Go to UniProtKB:  P0A7J7

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL2	FA [auth c]	273	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422  Go to UniProtKB:  P60422

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	GA [auth d]	209	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438  Go to UniProtKB:  P60438

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	HA [auth e]	201	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723  Go to UniProtKB:  P60723

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL5	IA [auth f]	179	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P62399 (Escherichia coli (strain K12)) Explore P62399  Go to UniProtKB:  P62399

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	JA [auth g]	177	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12)) Explore P0AG55  Go to UniProtKB:  P0AG55

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL9	KA [auth h]	149	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1  Go to UniProtKB:  P0A7R1

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	LA [auth i]	142	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10  Go to UniProtKB:  P0AA10

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL14	MA [auth j]	123	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3  Go to UniProtKB:  P0ADY3

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	NA [auth k]	144	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413  Go to UniProtKB:  P02413

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	OA [auth l]	136	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Explore P0ADY7  Go to UniProtKB:  P0ADY7

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	PA [auth m]	127	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44  Go to UniProtKB:  P0AG44

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL18	QA [auth n]	117	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018  Go to UniProtKB:  P0C018

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL19	RA [auth o]	115	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6  Go to UniProtKB:  P0A7K6

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	SA [auth p]	118	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3  Go to UniProtKB:  P0A7L3

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	TA [auth q]	103	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48  Go to UniProtKB:  P0AG48

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	UA [auth r]	110	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175  Go to UniProtKB:  P61175

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	VA [auth s]	100	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0  Go to UniProtKB:  P0ADZ0

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	WA [auth t]	104	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624  Go to UniProtKB:  P60624

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL25	XA [auth u]	94	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919  Go to UniProtKB:  P68919

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	YA [auth v]	85	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8  Go to UniProtKB:  P0A7L8

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL28	ZA [auth w]	78	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Explore P0A7M2  Go to UniProtKB:  P0A7M2

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	AB [auth x]	63	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Explore P0A7M6  Go to UniProtKB:  P0A7M6

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL30	BB [auth y]	59	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51  Go to UniProtKB:  P0AG51

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL32	CB [auth z]	57	Escherichia coli B	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4  Go to UniProtKB:  P0A7N4

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	A	1,554	Escherichia coli B

Entity ID: 22
Molecule	Chains	Length	Organism	Image
mRNA	V [auth X]	6	Escherichia coli B

Entity ID: 23
Molecule	Chains	Length	Organism	Image
P-site tRNA	W [auth Z]	77	Escherichia coli B

Entity ID: 29
Molecule	Chains	Length	Organism	Image
A-site tRNA	CA [auth 6]	2	Escherichia coli B

Entity ID: 30
Molecule	Chains	Length	Organism	Image
23S rRNA	DA [auth a]	2,908	Escherichia coli B

Entity ID: 31
Molecule	Chains	Length	Organism	Image
5S rRNA	EA [auth b]	120	Escherichia coli B

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AH [auth A], GH [auth 3], PX [auth a]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	AD [auth A], AF [auth A], AG [auth A], AJ [auth a], AL [auth a], AM [auth a], AQ [auth a], AR [auth a], AV [auth a], AW [auth a], AY [auth a], AZ [auth b], BD [auth A], BF [auth A], BG [auth A], BJ [auth a], BL [auth a], BM [auth a], BQ [auth a], BR [auth a], BU [auth a], BV [auth a], CD [auth A], CF [auth A], CG [auth A], CJ [auth a], CL [auth a], CM [auth a], CQ [auth a], CR [auth a], CV [auth a], DB [auth A], DD [auth A], DF [auth A], DH [auth D], DJ [auth a], DL [auth a], DM [auth a], DQ [auth a], DR [auth a], DV [auth a], DZ [auth c], EB [auth A], ED [auth A], EF [auth A], EG [auth A], EH [auth F], EJ [auth a], EL [auth a], EM [auth a], EN [auth a], EQ [auth a], ER [auth a], EV [auth a], FB [auth A], FD [auth A], FF [auth A], FJ [auth a], FL [auth a], FM [auth a], FQ [auth a], FR [auth a], FU [auth a], FV [auth a], FZ [auth c], GB [auth A], GD [auth A], GF [auth A], GI [auth a], GJ [auth a], GL [auth a], GM [auth a], GQ [auth a], GR [auth a], GV [auth a], GX [auth a], HB [auth A], HC [auth A], HD [auth A], HF [auth A], HJ [auth a], HL [auth a], HM [auth a], HQ [auth a], HR [auth a], HV [auth a], HZ [auth c], IC [auth A], ID [auth A], IF [auth A], IG [auth A], II [auth a], IJ [auth a], IL [auth a], IN [auth a], IQ [auth a], IR [auth a], IV [auth a], IX [auth a], IZ [auth c], JD [auth A], JF [auth A], JI [auth a], JJ [auth a], JL [auth a], JO [auth a], JQ [auth a], JR [auth a], JV [auth a], KF [auth A], KG [auth A], KJ [auth a], KL [auth a], KN [auth a], KQ [auth a], KR [auth a], KZ [auth d], LB [auth A], LC [auth A], LF [auth A], LH [auth a], LJ [auth a], LL [auth a], LN [auth a], LQ [auth a], LT [auth a], LX [auth a], LZ [auth e], MF [auth A], ML [auth a], MN [auth a], MQ [auth a], MT [auth a], MU [auth a], MY [auth a], MZ [auth f], NF [auth A], NL [auth a], NN [auth a], NQ [auth a], NT [auth a], OC [auth A], OL [auth a], ON [auth a], OQ [auth a], OT [auth a], PC [auth A], PJ [auth a], PK [auth a], PL [auth a], PQ [auth a], PT [auth a], PU [auth a], PW [auth a], PY [auth a], QC [auth A], QJ [auth a], QK [auth a], QL [auth a], QQ [auth a], QT [auth a], QU [auth a], RF [auth A], RI [auth a], RK [auth a], RL [auth a], RQ [auth a], RT [auth a], RU [auth a], SB [auth A], SC [auth A], SF [auth A], SK [auth a], SL [auth a], SQ [auth a], ST [auth a], SU [auth a], TC [auth A], TF [auth A], TI [auth a], TK [auth a], TL [auth a], TQ [auth a], TT [auth a], TU [auth a], TV [auth a], UC [auth A], UF [auth A], UI [auth a], UK [auth a], UL [auth a], UQ [auth a], UT [auth a], UU [auth a], VC [auth A], VE [auth A], VF [auth A], VK [auth a], VL [auth a], VQ [auth a], VU [auth a], WC [auth A], WF [auth A], WK [auth a], WL [auth a], WQ [auth a], WU [auth a], XC [auth A], XF [auth A], XH [auth a], XK [auth a], XL [auth a], XQ [auth a], XU [auth a], YC [auth A], YD [auth A], YE [auth A], YF [auth A], YG [auth A], YK [auth a], YL [auth a], YM [auth a], YQ [auth a], YU [auth a], ZC [auth A], ZE [auth A], ZF [auth A], ZK [auth a], ZL [auth a], ZQ [auth a], ZU [auth a]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	AC [auth A], AE [auth A], AI [auth a], AK [auth a], AN [auth a], AO [auth a], AP [auth a], AS [auth a], AT [auth a], AU [auth a], AX [auth a], BC [auth A], BE [auth A], BH [auth A], BI [auth a], BK [auth a], BN [auth a], BO [auth a], BP [auth a], BS [auth a], BT [auth a], BW [auth a], BX [auth a], BY [auth a], BZ [auth b], CC [auth A], CE [auth A], CH [auth B], CI [auth a], CK [auth a], CN [auth a], CO [auth a], CP [auth a], CS [auth a], CT [auth a], CU [auth a], CW [auth a], CX [auth a], CY [auth a], CZ [auth b], DC [auth A], DE [auth A], DG [auth A], DI [auth a], DK [auth a], DN [auth a], DO [auth a], DP [auth a], DS [auth a], DT [auth a], DU [auth a], DW [auth a], DX [auth a], DY [auth a], EC [auth A], EE [auth A], EI [auth a], EK [auth a], EO [auth a], EP [auth a], ES [auth a], ET [auth a], EU [auth a], EW [auth a], EX [auth a], EY [auth a], EZ [auth c], FC [auth A], FE [auth A], FG [auth A], FH [auth M], FI [auth a], FK [auth a], FN [auth a], FO [auth a], FP [auth a], FS [auth a], FT [auth a], FW [auth a], FX [auth a], FY [auth a], GC [auth A], GE [auth A], GG [auth A], GK [auth a], GN [auth a], GO [auth a], GP [auth a], GS [auth a], GT [auth a], GU [auth a], GW [auth a], GY [auth a], GZ [auth c], HE [auth A], HG [auth A], HH [auth a], HI [auth a], HK [auth a], HN [auth a], HO [auth a], HP [auth a], HS [auth a], HT [auth a], HU [auth a], HW [auth a], HX [auth a], HY [auth a], IB [auth A], IE [auth A], IH [auth a], IK [auth a], IM [auth a], IO [auth a], IP [auth a], IS [auth a], IT [auth a], IU [auth a], IW [auth a], IY [auth a], JB [auth A], JC [auth A], JE [auth A], JG [auth A], JH [auth a], JK [auth a], JM [auth a], JN [auth a], JP [auth a], JS [auth a], JT [auth a], JU [auth a], JW [auth a], JX [auth a], JY [auth a], JZ [auth d], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KH [auth a], KI [auth a], KK [auth a], KM [auth a], KO [auth a], KP [auth a], KS [auth a], KT [auth a], KU [auth a], KV [auth a], KW [auth a], KX [auth a], KY [auth a], LD [auth A], LE [auth A], LG [auth A], LI [auth a], LK [auth a], LM [auth a], LO [auth a], LP [auth a], LR [auth a], LS [auth a], LU [auth a], LV [auth a], LW [auth a], LY [auth a], MB [auth A], MC [auth A], MD [auth A], ME [auth A], MG [auth A], MH [auth a], MI [auth a], MJ [auth a], MK [auth a], MM [auth a], MO [auth a], MP [auth a], MR [auth a], MS [auth a], MV [auth a], MW [auth a], MX [auth a], NB [auth A], NC [auth A], ND [auth A], NE [auth A], NG [auth A], NH [auth a], NI [auth a], NJ [auth a], NK [auth a], NM [auth a], NO [auth a], NP [auth a], NR [auth a], NS [auth a], NU [auth a], NV [auth a], NW [auth a], NX [auth a], NY [auth a], NZ [auth k], OB [auth A], OD [auth A], OE [auth A], OF [auth A], OG [auth A], OH [auth a], OI [auth a], OJ [auth a], OK [auth a], OM [auth a], OO [auth a], OP [auth a], OR [auth a], OS [auth a], OU [auth a], OV [auth a], OW [auth a], OX [auth a], OY [auth a], OZ [auth p], PB [auth A], PD [auth A], PE [auth A], PF [auth A], PG [auth A], PH [auth a], PI [auth a], PM [auth a], PN [auth a], PO [auth a], PP [auth a], PR [auth a], PS [auth a], PV [auth a], PZ [auth z], QB [auth A], QD [auth A], QE [auth A], QF [auth A], QG [auth A], QH [auth a], QI [auth a], QM [auth a], QN [auth a], QO [auth a], QP [auth a], QR [auth a], QS [auth a], QV [auth a], QW [auth a], QX [auth a], QY [auth a], RB [auth A], RC [auth A], RD [auth A], RE [auth A], RG [auth A], RH [auth a], RJ [auth a], RM [auth a], RN [auth a], RO [auth a], RP [auth a], RR [auth a], RS [auth a], RV [auth a], RW [auth a], RX [auth a], RY [auth a], SD [auth A], SE [auth A], SG [auth A], SH [auth a], SI [auth a], SJ [auth a], SM [auth a], SN [auth a], SO [auth a], SP [auth a], SR [auth a], SS [auth a], SV [auth a], SW [auth a], SX [auth a], SY [auth a], TB [auth A], TD [auth A], TE [auth A], TG [auth A], TH [auth a], TJ [auth a], TM [auth a], TN [auth a], TO [auth a], TP [auth a], TR [auth a], TS [auth a], TW [auth a], TX [auth a], TY [auth a], UB [auth A], UD [auth A], UE [auth A], UG [auth A], UH [auth a], UJ [auth a], UM [auth a], UN [auth a], UO [auth a], UP [auth a], UR [auth a], US [auth a], UV [auth a], UW [auth a], UX [auth a], UY [auth a], VB [auth A], VD [auth A], VG [auth A], VH [auth a], VI [auth a], VJ [auth a], VM [auth a], VN [auth a], VO [auth a], VP [auth a], VR [auth a], VS [auth a], VT [auth a], VV [auth a], VW [auth a], VX [auth a], VY [auth a], WB [auth A], WD [auth A], WE [auth A], WG [auth A], WH [auth a], WI [auth a], WJ [auth a], WM [auth a], WN [auth a], WO [auth a], WP [auth a], WR [auth a], WS [auth a], WT [auth a], WV [auth a], WW [auth a], WX [auth a], WY [auth b], XB [auth A], XD [auth A], XE [auth A], XG [auth A], XI [auth a], XJ [auth a], XM [auth a], XN [auth a], XO [auth a], XP [auth a], XR [auth a], XS [auth a], XT [auth a], XV [auth a], XW [auth a], XX [auth a], XY [auth b], YB [auth A], YH [auth a], YI [auth a], YJ [auth a], YN [auth a], YO [auth a], YP [auth a], YR [auth a], YS [auth a], YT [auth a], YV [auth a], YW [auth a], YX [auth a], YY [auth b], ZB [auth A], ZD [auth A], ZG [auth A], ZH [auth a], ZI [auth a], ZJ [auth a], ZM [auth a], ZN [auth a], ZO [auth a], ZP [auth a], ZR [auth a], ZS [auth a], ZT [auth a], ZV [auth a], ZW [auth a], ZX [auth a], ZY [auth b]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
D2T	L	L-PEPTIDE LINKING	C5 H9 N O4 S		ASP
MEQ	GA [auth d]	L-PEPTIDE LINKING	C6 H12 N2 O3		GLN
4D4	OA [auth l]	L-PEPTIDE LINKING	C6 H14 N4 O3		ARG

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Diffraction Data: https://doi.org/10.6019/EMPIAR-11377

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev_5505

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Leonarski, f., Henning-Knechtel, A., Kirmizialtin, S., Ennifar, E., Auffinger, P.

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Funding Organization	Location	Grant Number
Centre National de la Recherche Scientifique (CNRS)	France	--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release