8ZFF | pdb_00008zff

Structure of the Bacterial Ribosome without hypoxia-induced rRNA modifications

• PDB DOI: https://doi.org/10.2210/pdb8ZFF/pdb
• EM Map EMD-60059: EMDB EMDataResource
• NAKB: 8ZFF

• Classification: RIBOSOME
• Organism(s): Escherichia coli BW25113, Escherichia phage T4
• Mutation(s): No 


• Deposited: 2024-05-07 Released: 2025-11-12 
• Deposition Author(s): Ishiguro, K., Yokoyama, T., Shirouzu, M., Ito, T., Suzuki, T.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Novel rRNA methylations regulate translational efficiency of the ribosomes in response to oxygen condition

Ishiguro, K., Midorikawa, K., Miyauchi, K., Kimura, S., Naoki, S., Yokoyama, T., Shirouzu, M., Liiv, A., Remme, J., Ito, T., Suzuki, T.

To be published.

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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,197.67 kDa 
• Atom Count: 140,322 
• Modeled Residue Count: 10,062 
• Deposited Residue Count: 10,622 
• Unique protein chains: 49
• Unique nucleic acid chains: 5

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS2	B	241	Escherichia coli BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 BW25113	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 uL2	X [auth c]	273	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422  Go to UniProtKB:  P60422

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL3	Y [auth d]	209	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438  Go to UniProtKB:  P60438

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	Z [auth e]	201	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723  Go to UniProtKB:  P60723

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL5	AA [auth f]	179	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P62399 (Escherichia coli (strain K12)) Explore P62399  Go to UniProtKB:  P62399

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	BA [auth g]	177	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12)) Explore P0AG55  Go to UniProtKB:  P0AG55

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL9	CA [auth h]	149	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1  Go to UniProtKB:  P0A7R1

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	DA [auth i]	142	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10  Go to UniProtKB:  P0AA10

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL14	EA [auth j]	123	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3  Go to UniProtKB:  P0ADY3

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	FA [auth k]	144	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413  Go to UniProtKB:  P02413

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	GA [auth l]	136	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Explore P0ADY7  Go to UniProtKB:  P0ADY7

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	HA [auth m]	127	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44  Go to UniProtKB:  P0AG44

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL18	IA [auth n]	117	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018  Go to UniProtKB:  P0C018

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL19	JA [auth o]	115	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6  Go to UniProtKB:  P0A7K6

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	KA [auth p]	118	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3  Go to UniProtKB:  P0A7L3

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	LA [auth q]	103	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48  Go to UniProtKB:  P0AG48

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	MA [auth r]	110	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175  Go to UniProtKB:  P61175

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	NA [auth s]	100	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0  Go to UniProtKB:  P0ADZ0

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	OA [auth t]	104	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624  Go to UniProtKB:  P60624

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL25	PA [auth u]	94	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919  Go to UniProtKB:  P68919

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	QA [auth v]	85	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8  Go to UniProtKB:  P0A7L8

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL28	RA [auth w]	78	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Explore P0A7M2  Go to UniProtKB:  P0A7M2

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	SA [auth x]	63	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Explore P0A7M6  Go to UniProtKB:  P0A7M6

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL30	TA [auth y]	59	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51  Go to UniProtKB:  P0AG51

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL32	UA [auth z]	57	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4  Go to UniProtKB:  P0A7N4

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL33	VA [auth 0]	55	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Explore P0A7N9  Go to UniProtKB:  P0A7N9

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL34	WA [auth 1]	46	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5  Go to UniProtKB:  P0A7P5

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL35	XA [auth 2]	65	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1  Go to UniProtKB:  P0A7Q1

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL36A	YA [auth 3]	38	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Explore P0A7Q6  Go to UniProtKB:  P0A7Q6

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL31	ZA [auth 4]	70	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S rRNA	A	1,542	Escherichia coli BW25113

Entity ID: 22
Molecule	Chains	Length	Organism	Image
23S rRNA	V [auth a]	2,904	Escherichia coli BW25113

Entity ID: 23
Molecule	Chains	Length	Organism	Image
5S rRNA	W [auth b]	120	Escherichia coli BW25113

Entity ID: 53
Molecule	Chains	Length	Organism	Image
mRNA	AB [auth X]	66	Escherichia phage T4

Entity ID: 54
Molecule	Chains	Length	Organism	Image
P-site tRNA-fMet	BB [auth Z]	77	Escherichia coli BW25113

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	AC [auth A], AD [auth A], AE [auth A], AF [auth A], AG [auth a], AH [auth a], AI [auth a], AJ [auth a], AK [auth a], AL [auth a], AM [auth a], AN [auth a], AO [auth a], AP [auth a], AQ [auth a], AR [auth a], AS [auth a], BC [auth A], BD [auth A], BE [auth A], BF [auth A], BG [auth a], BH [auth a], BI [auth a], BJ [auth a], BK [auth a], BL [auth a], BM [auth a], BN [auth a], BO [auth a], BP [auth a], BQ [auth a], BR [auth a], BS [auth a], CB [auth A], CC [auth A], CD [auth A], CE [auth A], CF [auth A], CG [auth a], CH [auth a], CI [auth a], CJ [auth a], CK [auth a], CL [auth a], CM [auth a], CN [auth a], CO [auth a], CP [auth a], CQ [auth a], CR [auth a], CS [auth a], DB [auth A], DC [auth A], DD [auth A], DE [auth A], DF [auth A], DG [auth a], DH [auth a], DI [auth a], DJ [auth a], DK [auth a], DL [auth a], DM [auth a], DN [auth a], DO [auth a], DP [auth a], DQ [auth a], DR [auth a], DS [auth a], EB [auth A], EC [auth A], ED [auth A], EE [auth A], EF [auth A], EG [auth a], EH [auth a], EI [auth a], EJ [auth a], EK [auth a], EL [auth a], EM [auth a], EN [auth a], EO [auth a], EP [auth a], EQ [auth a], ER [auth a], ES [auth a], FB [auth A], FC [auth A], FD [auth A], FE [auth A], FF [auth A], FG [auth a], FH [auth a], FI [auth a], FJ [auth a], FK [auth a], FL [auth a], FM [auth a], FN [auth a], FO [auth a], FP [auth a], FQ [auth a], FR [auth a], FS [auth a], GB [auth A], GC [auth A], GD [auth A], GE [auth A], GF [auth A], GG [auth a], GH [auth a], GI [auth a], GJ [auth a], GK [auth a], GL [auth a], GM [auth a], GN [auth a], GO [auth a], GP [auth a], GQ [auth a], GR [auth a], GS [auth a], HB [auth A], HC [auth A], HD [auth A], HE [auth A], HF [auth A], HG [auth a], HH [auth a], HI [auth a], HJ [auth a], HK [auth a], HL [auth a], HM [auth a], HN [auth a], HO [auth a], HP [auth a], HQ [auth a], HR [auth a], HS [auth b], IB [auth A], IC [auth A], ID [auth A], IE [auth A], IF [auth A], IG [auth a], IH [auth a], II [auth a], IJ [auth a], IK [auth a], IL [auth a], IM [auth a], IN [auth a], IO [auth a], IP [auth a], IQ [auth a], IR [auth a], IS [auth b], JB [auth A], JC [auth A], JD [auth A], JE [auth A], JF [auth A], JG [auth a], JH [auth a], JI [auth a], JJ [auth a], JK [auth a], JL [auth a], JM [auth a], JN [auth a], JO [auth a], JP [auth a], JQ [auth a], JR [auth a], JS [auth b], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KF [auth A], KG [auth a], KH [auth a], KI [auth a], KJ [auth a], KK [auth a], KL [auth a], KM [auth a], KN [auth a], KO [auth a], KP [auth a], KQ [auth a], KR [auth a], KS [auth b], LB [auth A], LC [auth A], LD [auth A], LE [auth A], LF [auth A], LG [auth a], LH [auth a], LI [auth a], LJ [auth a], LK [auth a], LL [auth a], LM [auth a], LN [auth a], LO [auth a], LP [auth a], LQ [auth a], LR [auth a], LS [auth b], MB [auth A], MC [auth A], MD [auth A], ME [auth A], MF [auth A], MG [auth a], MH [auth a], MI [auth a], MJ [auth a], MK [auth a], ML [auth a], MM [auth a], MN [auth a], MO [auth a], MP [auth a], MQ [auth a], MR [auth a], MS [auth b], NB [auth A], NC [auth A], ND [auth A], NE [auth A], NF [auth A], NG [auth a], NH [auth a], NI [auth a], NJ [auth a], NK [auth a], NL [auth a], NM [auth a], NN [auth a], NO [auth a], NP [auth a], NQ [auth a], NR [auth a], NS [auth c], OB [auth A], OC [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], OL [auth a], OM [auth a], ON [auth a], OO [auth a], OP [auth a], OQ [auth a], OR [auth a], OS [auth d], PB [auth A], PC [auth A], PD [auth A], PE [auth A], PF [auth A], PG [auth a], PH [auth a], PI [auth a], PJ [auth a], PK [auth a], PL [auth a], PM [auth a], PN [auth a], PO [auth a], PP [auth a], PQ [auth a], PR [auth a], PS [auth z], QB [auth A], QC [auth A], QD [auth A], QE [auth A], QF [auth A], QG [auth a], QH [auth a], QI [auth a], QJ [auth a], QK [auth a], QL [auth a], QM [auth a], QN [auth a], QO [auth a], QP [auth a], QQ [auth a], QR [auth a], QS [auth Z], RB [auth A], RC [auth A], RD [auth A], RE [auth A], RF [auth a], RG [auth a], RH [auth a], RI [auth a], RJ [auth a], RK [auth a], RL [auth a], RM [auth a], RN [auth a], RO [auth a], RP [auth a], RQ [auth a], RR [auth a], SB [auth A], SC [auth A], SD [auth A], SE [auth A], SF [auth a], SG [auth a], SH [auth a], SI [auth a], SJ [auth a], SK [auth a], SL [auth a], SM [auth a], SN [auth a], SO [auth a], SP [auth a], SQ [auth a], SR [auth a], TB [auth A], TC [auth A], TD [auth A], TE [auth A], TF [auth a], TG [auth a], TH [auth a], TI [auth a], TJ [auth a], TK [auth a], TL [auth a], TM [auth a], TN [auth a], TO [auth a], TP [auth a], TQ [auth a], TR [auth a], UB [auth A], UC [auth A], UD [auth A], UE [auth A], UF [auth a], UG [auth a], UH [auth a], UI [auth a], UJ [auth a], UK [auth a], UL [auth a], UM [auth a], UN [auth a], UO [auth a], UP [auth a], UQ [auth a], UR [auth a], VB [auth A], VC [auth A], VD [auth A], VE [auth A], VF [auth a], VG [auth a], VH [auth a], VI [auth a], VJ [auth a], VK [auth a], VL [auth a], VM [auth a], VN [auth a], VO [auth a], VP [auth a], VQ [auth a], VR [auth a], WB [auth A], WC [auth A], WD [auth A], WE [auth A], WF [auth a], WG [auth a], WH [auth a], WI [auth a], WJ [auth a], WK [auth a], WL [auth a], WM [auth a], WN [auth a], WO [auth a], WP [auth a], WQ [auth a], WR [auth a], XB [auth A], XC [auth A], XD [auth A], XE [auth A], XF [auth a], XG [auth a], XH [auth a], XI [auth a], XJ [auth a], XK [auth a], XL [auth a], XM [auth a], XN [auth a], XO [auth a], XP [auth a], XQ [auth a], XR [auth a], YB [auth A], YC [auth A], YD [auth A], YE [auth A], YF [auth a], YG [auth a], YH [auth a], YI [auth a], YJ [auth a], YK [auth a], YL [auth a], YM [auth a], YN [auth a], YO [auth a], YP [auth a], YQ [auth a], YR [auth a], ZB [auth A], ZC [auth A], ZD [auth A], ZE [auth A], ZF [auth a], ZG [auth a], ZH [auth a], ZI [auth a], ZJ [auth a], ZK [auth a], ZL [auth a], ZM [auth a], ZN [auth a], ZO [auth a], ZP [auth a], ZQ [auth a], ZR [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
D2T	L	L-PEPTIDE LINKING	C5 H9 N O4 S		ASP
MEQ	Y [auth d]	L-PEPTIDE LINKING	C6 H12 N2 O3		GLN
4D4	GA [auth l]	L-PEPTIDE LINKING	C6 H14 N4 O3		ARG
MS6	GA [auth l]	L-PEPTIDE LINKING	C5 H11 N O S2		MET

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.3
MODEL REFINEMENT	PHENIX	1.18
MODEL REFINEMENT	Coot	0.9.5

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Ishiguro, K., Yokoyama, T., Shirouzu, M., Ito, T., Suzuki, T.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--
Japan Society for the Promotion of Science (JSPS)	Japan	26113003, 26220205 and 18H05272
Japan Science and Technology	Japan	JPMJER2002

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release
  
• Version 2.0: 2025-12-24
  Changes: Data collection, Non-polymer description, Structure summary