9IOT | pdb_00009iot

Cryo-EM structure of Escherichia coli hibernating ribosome with RNase I mutant

• PDB DOI: https://doi.org/10.2210/pdb9IOT/pdb
• NAKB: 9IOT
• EM Map EMD-60747: EMDB EMDataResource

• Classification: RIBOSOME
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-07-09 Released: 2025-07-30 
• Deposition Author(s): Tanzawa, T., Minami, A., Yoshida, H., Kato, T., Ogawa, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis of RNase I-mediated rRNA degradation regulated by ribosomes

Minami, A., Tanzawa, T., Miyata, T., Makino, F., Yang, Z., Funatsu, T., Kuzuyama, T., Yoshida, H., Kato, T., Ogawa, T.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2024.07.29.605612

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 53-mer - AA1AB1AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 53-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1z1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2,244.63 kDa 
• Atom Count: 143,360 
• Modeled Residue Count: 10,557 
• Deposited Residue Count: 11,309 
• Unique protein chains: 53
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	A [auth 0]	63	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Explore P0A7M6  Go to UniProtKB:  P0A7M6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL30	B [auth 1]	59	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51  Go to UniProtKB:  P0AG51

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL32	C [auth 3]	57	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4  Go to UniProtKB:  P0A7N4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL33	D [auth 4]	55	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Explore P0A7N9  Go to UniProtKB:  P0A7N9

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	E [auth 5]	46	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5  Go to UniProtKB:  P0A7P5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL35	F [auth 6]	65	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1  Go to UniProtKB:  P0A7Q1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	G [auth 7]	38	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Explore P0A7Q6  Go to UniProtKB:  P0A7Q6

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL2	I [auth D]	273	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422  Go to UniProtKB:  P60422

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	J [auth E]	209	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438  Go to UniProtKB:  P60438

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	K [auth F]	201	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723  Go to UniProtKB:  P60723

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL5	L [auth G]	179	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P62399 (Escherichia coli (strain K12)) Explore P62399  Go to UniProtKB:  P62399

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	M [auth H]	177	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12)) Explore P0AG55  Go to UniProtKB:  P0AG55

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL9	N [auth I]	41	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1  Go to UniProtKB:  P0A7R1

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	O [auth L]	142	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10  Go to UniProtKB:  P0AA10

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	P [auth M]	123	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3  Go to UniProtKB:  P0ADY3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	Q [auth N]	144	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A7ZSJ0 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZSJ0  Go to UniProtKB:  A7ZSJ0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL16	R [auth O]	136	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Explore P0ADY7  Go to UniProtKB:  P0ADY7

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	S [auth P]	127	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44  Go to UniProtKB:  P0AG44

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL18	T [auth Q]	117	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018  Go to UniProtKB:  P0C018

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL19	U [auth R]	115	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6  Go to UniProtKB:  P0A7K6

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	V [auth S]	118	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3  Go to UniProtKB:  P0A7L3

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	W [auth T]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48  Go to UniProtKB:  P0AG48

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	X [auth U]	110	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175  Go to UniProtKB:  P61175

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	Y [auth V]	100	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0  Go to UniProtKB:  P0ADZ0

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	Z [auth W]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624  Go to UniProtKB:  P60624

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	AA [auth X]	94	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919  Go to UniProtKB:  P68919

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	BA [auth Y]	85	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8  Go to UniProtKB:  P0A7L8

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL28	CA [auth Z]	78	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Explore P0A7M2  Go to UniProtKB:  P0A7M2

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL31	DA [auth 2]	67	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS2	GA [auth b]	241	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A7ZHQ9 (Escherichia coli O139:H28 (strain E24377A / ETEC)) Explore A7ZHQ9  Go to UniProtKB:  A7ZHQ9

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS3	HA [auth c]	233	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Explore P0A7V3  Go to UniProtKB:  P0A7V3

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS4	IA [auth d]	206	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Explore P0A7V8  Go to UniProtKB:  P0A7V8

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS5	JA [auth e]	167	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Explore P0A7W1  Go to UniProtKB:  P0A7W1

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS6, fully modified isoform	KA [auth f]	102	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358  Go to UniProtKB:  P02358

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS7	LA [auth g]	179	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P02359 (Escherichia coli (strain K12)) Explore P02359  Go to UniProtKB:  P02359

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS8	MA [auth h]	130	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7  Go to UniProtKB:  P0A7W7

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS9	NA [auth i]	130	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Explore P0A7X3  Go to UniProtKB:  P0A7X3

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS10	OA [auth j]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Explore P0A7R5  Go to UniProtKB:  P0A7R5

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS11	PA [auth k]	129	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Explore P0A7R9  Go to UniProtKB:  P0A7R9

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS12	QA [auth l]	124	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Explore P0A7S3  Go to UniProtKB:  P0A7S3

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS13	RA [auth m]	118	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Explore P0A7S9  Go to UniProtKB:  P0A7S9

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS14	SA [auth n]	101	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12)) Explore P0AG59  Go to UniProtKB:  P0AG59

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS15	TA [auth o]	89	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12)) Explore P0ADZ4  Go to UniProtKB:  P0ADZ4

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS16	UA [auth p]	82	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Explore P0A7T3  Go to UniProtKB:  P0A7T3

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS17	VA [auth q]	84	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12)) Explore P0AG63  Go to UniProtKB:  P0AG63

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS18	WA [auth r]	75	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7  Go to UniProtKB:  P0A7T7

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS19	XA [auth s]	92	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Explore P0A7U3  Go to UniProtKB:  P0A7U3

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS20	YA [auth t]	87	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7  Go to UniProtKB:  P0A7U7

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	ZA [auth u]	71	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P68679 (Escherichia coli (strain K12)) Explore P68679  Go to UniProtKB:  P68679

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome hibernation promoting factor	AB [auth v]	95	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AFX0 (Escherichia coli (strain K12)) Explore P0AFX0  Go to UniProtKB:  P0AFX0

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome modulation factor	BB [auth y]	55	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AFW2 (Escherichia coli (strain K12)) Explore P0AFW2  Go to UniProtKB:  P0AFW2

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease I	CB [auth z]	268	Escherichia coli	Mutation(s): 2  Gene Names: rna, rnsA, b0611, JW0603 EC: 4.6.1.21
UniProt
Find proteins for P21338 (Escherichia coli (strain K12)) Explore P21338  Go to UniProtKB:  P21338

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS1	DB [auth 8]	557	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG67 (Escherichia coli (strain K12)) Explore P0AG67  Go to UniProtKB:  P0AG67

Entity ID: 8
Molecule	Chains	Length	Organism	Image
5S rRNA	H [auth B]	120	Escherichia coli

Entity ID: 31
Molecule	Chains	Length	Organism	Image
23S rRNA	EA [auth A]	2,904	Escherichia coli

Entity ID: 32
Molecule	Chains	Length	Organism	Image
16S rRNA	FA [auth a]	1,542	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	LT [auth z]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	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], AT [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], BT [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], CT [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], DT [auth a], EB [auth 3], 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], ET [auth a], FB [auth B], 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], FT [auth a], GB [auth B], 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], GT [auth a], HB [auth B], 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 a], HT [auth a], IB [auth B], 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 a], IT [auth a], JB [auth B], 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 a], JT [auth a], KB [auth B], 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 a], KT [auth a], LB [auth D], 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 a], MB [auth D], 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 a], NB [auth E], 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 a], OB [auth O], 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 a], 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 a], 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 a], 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], RS [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], SS [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], TS [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], US [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], VS [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], WS [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], XS [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], YS [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], ZS [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.0.0
MODEL REFINEMENT	Servalcat	0.4.74

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Tanzawa, T., Minami, A., Yoshida, H., Kato, T., Ogawa, T.

---

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121001
Japan Society for the Promotion of Science (JSPS)	Japan	20K21266

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release