8FZI

Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-B)

• PDB DOI: https://doi.org/10.2210/pdb8FZI/pdb
• NAKB: 8FZI
• EM Map EMD-29631: EMDB EMDataResource

• Classification: RIBOSOME
• Organism(s): Escherichia coli, Escherichia phage T4, Escherichia coli K-12
• Expression System: Escherichia coli HB101, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-28 Released: 2024-07-17 
• Deposition Author(s): Rybak, M.Y., Li, L., Lin, J., Gagnon, M.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

The ribosome termination complex remodels release factor RF3 and ejects GDP.

Li, L., Rybak, M.Y., Lin, J., Gagnon, M.G.

(2024) Nat Struct Mol Biol 

• PubMed: 39030416 
• DOI: https://doi.org/10.1038/s41594-024-01360-0
• Primary Citation of Related Structures:  
  8FZD, 8FZE, 8FZF, 8FZG, 8FZH, 8FZI, 8FZJ


• PubMed Abstract: 
  

  Translation termination involves release factors RF1, RF2 and the GTPase RF3 that recycles RF1 and RF2 from the ribosome. RF3 dissociates from the ribosome in the GDP-bound form and must then exchange GDP for GTP. The 70S ribosome termination complex (70S-TC) accelerates GDP exchange in RF3, suggesting that the 70S-TC can function as the guanine nucleotide exchange factor for RF3. Here, we use cryogenic-electron microscopy to elucidate the mechanism of GDP dissociation from RF3 catalyzed by the Escherichia coli 70S-TC. The non-rotated ribosome bound to RF1 remodels RF3 and induces a peptide flip in the phosphate-binding loop, efficiently ejecting GDP. Binding of GTP allows RF3 to dock at the GTPase center, promoting the dissociation of RF1 from the ribosome. The structures recapitulate the functional cycle of RF3 on the ribosome and uncover the mechanism by which the 70S-TC allosterically dismantles the phosphate-binding groove in RF3, a previously overlooked function of the ribosome.

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Organizational Affiliation: 

State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 51-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 51-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2,264.1 kDa 
• Atom Count: 149,604 
• Modelled Residue Count: 10,925 
• Deposited Residue Count: 11,236 
• Unique protein chains: 51
• Unique nucleic acid chains: 5

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B [auth b]	241	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for J7QM75 (Escherichia coli) Explore J7QM75  Go to UniProtKB:  J7QM75

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C [auth c]	233	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for B7MCS9 (Escherichia coli O45:K1 (strain S88 / ExPEC)) Explore B7MCS9  Go to UniProtKB:  B7MCS9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D [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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	E [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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	F [auth f]	131	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for C3SFQ7 (Escherichia coli) Explore C3SFQ7  Go to UniProtKB:  C3SFQ7

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G [auth g]	156	Escherichia coli	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
30S ribosomal protein S8	H [auth h]	130	Escherichia coli	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I [auth i]	130	Escherichia coli	Mutation(s): 0

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J [auth j]	103	Escherichia coli	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K [auth k]	129	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A0H3PWX2 (Escherichia coli O157:H7 (strain EC869)) Explore A0A0H3PWX2  Go to UniProtKB:  A0A0H3PWX2

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L [auth l]	124	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A0F1AUC4 (Enterobacter sichuanensis) Explore A0A0F1AUC4  Go to UniProtKB:  A0A0F1AUC4

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M [auth m]	118	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A7U9IV78 (Escherichia coli HVH 36) Explore A0A7U9IV78  Go to UniProtKB:  A0A7U9IV78

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	N [auth n]	101	Escherichia coli	Mutation(s): 0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O [auth o]	89	Escherichia coli	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P [auth p]	82	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for C3SYP2 (Escherichia coli) Explore C3SYP2  Go to UniProtKB:  C3SYP2

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	Q [auth q]	84	Escherichia coli	Mutation(s): 0

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R [auth r]	75	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A0E2KXL3 (Escherichia coli (strain UMEA 3162-1)) Explore A0A0E2KXL3  Go to UniProtKB:  A0A0E2KXL3

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	S [auth s]	92	Escherichia coli	Mutation(s): 0

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	T [auth t]	87	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for C3TRH7 (Escherichia coli) Explore C3TRH7  Go to UniProtKB:  C3TRH7

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	U [auth u]	71	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A0E2L2J1 (Escherichia coli (strain UMEA 3162-1)) Explore A0A0E2L2J1  Go to UniProtKB:  A0A0E2L2J1

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide chain release factor RF3	X [auth v]	529	Escherichia coli K-12	Mutation(s): 0  Gene Names: prfC, miaD, tos, b4375, JW5873
UniProt
Find proteins for P0A7I4 (Escherichia coli (strain K12)) Explore P0A7I4  Go to UniProtKB:  P0A7I4

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	AA [auth C]	273	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422  Go to UniProtKB:  P60422

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	BA [auth D]	209	Escherichia coli	Mutation(s): 0

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	CA [auth E]	201	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A1AGK6 (Escherichia coli O1:K1 / APEC) Explore A1AGK6  Go to UniProtKB:  A1AGK6

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	DA [auth F]	179	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A140N5A3 (Escherichia coli (strain B / BL21-DE3)) Explore A0A140N5A3  Go to UniProtKB:  A0A140N5A3

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	EA [auth G]	177	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for C3SR17 (Escherichia coli) Explore C3SR17  Go to UniProtKB:  C3SR17

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	FA [auth I]	165	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7J3 (Escherichia coli (strain K12)) Explore P0A7J3  Go to UniProtKB:  P0A7J3

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	GA [auth J]	142	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12)) Explore P0A7J7  Go to UniProtKB:  P0A7J7

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	HA [auth L]	142	Escherichia coli	Mutation(s): 0

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	IA [auth M]	123	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for S1NW45 (Escherichia coli KTE182) Explore S1NW45  Go to UniProtKB:  S1NW45

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	JA [auth N]	144	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for Q1R630 (Escherichia coli (strain UTI89 / UPEC)) Explore Q1R630  Go to UniProtKB:  Q1R630

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	KA [auth O]	136	Escherichia coli	Mutation(s): 0

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	LA [auth P]	127	Escherichia coli	Mutation(s): 0

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	MA [auth Q]	117	Escherichia coli	Mutation(s): 0

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	NA [auth R]	115	Escherichia coli	Mutation(s): 0

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	OA [auth S]	118	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for B7MAS6 (Escherichia coli O45:K1 (strain S88 / ExPEC)) Explore B7MAS6  Go to UniProtKB:  B7MAS6

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L21	PA [auth T]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for C3SSG2 (Escherichia coli) Explore C3SSG2  Go to UniProtKB:  C3SSG2

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	QA [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: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	RA [auth V]	100	Escherichia coli	Mutation(s): 0

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	SA [auth W]	104	Escherichia coli	Mutation(s): 0

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	TA [auth X]	94	Escherichia coli	Mutation(s): 0

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	UA [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: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	VA [auth Z]	78	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A1X3JA73 (Escherichia coli H386) Explore A0A1X3JA73  Go to UniProtKB:  A0A1X3JA73

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	WA [auth 1]	63	Escherichia coli	Mutation(s): 0

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	XA [auth 2]	59	Escherichia coli	Mutation(s): 0

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	YA [auth 3]	70	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	ZA [auth 4]	57	Escherichia coli	Mutation(s): 0

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	AB [auth 5]	55	Escherichia coli	Mutation(s): 0

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	BB [auth 6]	46	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for B7MGC4 (Escherichia coli O45:K1 (strain S88 / ExPEC)) Explore B7MGC4  Go to UniProtKB:  B7MGC4

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	CB [auth 7]	65	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1  Go to UniProtKB:  P0A7Q1

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	DB [auth 8]	38	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1)) Explore A0A0E2L017  Go to UniProtKB:  A0A0E2L017

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S Ribosomal RNA	A [auth a]	1,542	Escherichia coli

Entity ID: 22
Molecule	Chains	Length	Organism	Image
p/E phenylalanyl-tRNA	V [auth x]	76	Escherichia coli

Entity ID: 23
Molecule	Chains	Length	Organism	Image
F-UAA mRNA	W [auth z]	21	Escherichia phage T4

Entity ID: 25
Molecule	Chains	Length	Organism	Image
23S Ribosomal RNA	Y [auth A]	2,904	Escherichia coli

Entity ID: 26
Molecule	Chains	Length	Organism	Image
5S Ribosomal RNA	Z [auth B]	120	Escherichia coli

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCP	DG [auth v]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C11 H18 N5 O13 P3 PHBDHXOBFUBCJD-KQYNXXCUSA-N
ZN	LDA [auth 3], PDA [auth 8]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth A], ABA [auth A], AC [auth a], ACA [auth A], AD [auth a], ADA [auth E], AE [auth a], AF [auth a], AG [auth p], 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], AU [auth A], AV [auth A], AW [auth A], AX [auth A], AY [auth A], AZ [auth A], BAA [auth A], BBA [auth A], BC [auth a], BCA [auth A], BD [auth a], BDA [auth N], BE [auth a], BF [auth a], BG [auth x], 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], BU [auth A], BV [auth A], BW [auth A], BX [auth A], BY [auth A], BZ [auth A], CAA [auth A], CBA [auth A], CC [auth a], CCA [auth A], CD [auth a], CDA [auth P], CE [auth a], CF [auth a], CG [auth z], 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], CU [auth A], CV [auth A], CW [auth A], CX [auth A], CY [auth A], CZ [auth A], DAA [auth A], DBA [auth A], DC [auth a], DCA [auth A], DD [auth a], DDA [auth P], DE [auth a], DF [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], DU [auth A], DV [auth A], DW [auth A], DX [auth A], DY [auth A], DZ [auth A], EAA [auth A], EB [auth a], EBA [auth A], EC [auth a], ECA [auth B], ED [auth a], EDA [auth S], 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], EU [auth A], EV [auth A], EW [auth A], EX [auth A], EY [auth A], EZ [auth A], FAA [auth A], FB [auth a], FBA [auth A], FC [auth a], FCA [auth B], FD [auth a], FDA [auth T], 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], FU [auth A], FV [auth A], FW [auth A], FX [auth A], FY [auth A], FZ [auth A], GAA [auth A], GB [auth a], GBA [auth A], GC [auth a], GCA [auth B], GD [auth a], GDA [auth T], 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], GU [auth A], GV [auth A], GW [auth A], GX [auth A], GY [auth A], GZ [auth A], HAA [auth A], HB [auth a], HBA [auth A], HC [auth a], HCA [auth B], HD [auth a], HDA [auth T], 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], HU [auth A], HV [auth A], HW [auth A], HX [auth A], HY [auth A], HZ [auth A], IAA [auth A], IB [auth a], IBA [auth A], IC [auth a], ICA [auth B], ID [auth a], IDA [auth V], 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], IU [auth A], IV [auth A], IW [auth A], IX [auth A], IY [auth A], IZ [auth A], JAA [auth A], JB [auth a], JBA [auth A], JC [auth a], JCA [auth B], JD [auth a], JDA [auth V], 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], JU [auth A], JV [auth A], JW [auth A], JX [auth A], JY [auth A], JZ [auth A], KAA [auth A], KB [auth a], KBA [auth A], KC [auth a], KCA [auth B], KD [auth a], KDA [auth Y], 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], KU [auth A], KV [auth A], KW [auth A], KX [auth A], KY [auth A], KZ [auth A], LAA [auth A], LB [auth a], LBA [auth A], LC [auth a], LCA [auth B], 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], LT [auth A], LU [auth A], LV [auth A], LW [auth A], LX [auth A], LY [auth A], LZ [auth A], MAA [auth A], MB [auth a], MBA [auth A], MC [auth a], MCA [auth B], MD [auth a], MDA [auth 4], 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], MT [auth A], MU [auth A], MV [auth A], MW [auth A], MX [auth A], MY [auth A], MZ [auth A], NAA [auth A], NB [auth a], NBA [auth A], NC [auth a], NCA [auth B], ND [auth a], NDA [auth 6], 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], NT [auth A], NU [auth A], NV [auth A], NW [auth A], NX [auth A], NY [auth A], NZ [auth A], OAA [auth A], OB [auth a], OBA [auth A], OC [auth a], OCA [auth B], OD [auth a], ODA [auth 7], 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], OT [auth A], OU [auth A], OV [auth A], OW [auth A], OX [auth A], OY [auth A], OZ [auth A], PAA [auth A], PB [auth a], PBA [auth A], PC [auth a], PCA [auth B], 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], PT [auth A], PU [auth A], PV [auth A], PW [auth A], PX [auth A], PY [auth A], PZ [auth A], QAA [auth A], QB [auth a], QBA [auth A], QC [auth a], QCA [auth B], 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], QT [auth A], QU [auth A], QV [auth A], QW [auth A], QX [auth A], QY [auth A], QZ [auth A], RAA [auth A], RB [auth a], RBA [auth A], RC [auth a], RCA [auth B], 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], RT [auth A], RU [auth A], RV [auth A], RW [auth A], RX [auth A], RY [auth A], RZ [auth A], SAA [auth A], SB [auth a], SBA [auth A], SC [auth a], SCA [auth B], 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], ST [auth A], SU [auth A], SV [auth A], SW [auth A], SX [auth A], SY [auth A], SZ [auth A], TAA [auth A], TB [auth a], TBA [auth A], TC [auth a], TCA [auth C], 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], TT [auth A], TU [auth A], TV [auth A], TW [auth A], TX [auth A], TY [auth A], TZ [auth A], UAA [auth A], UB [auth a], UBA [auth A], UC [auth a], UCA [auth C], 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], UT [auth A], UU [auth A], UV [auth A], UW [auth A], UX [auth A], UY [auth A], UZ [auth A], VAA [auth A], VB [auth a], VBA [auth A], VC [auth a], VCA [auth C], 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], VT [auth A], VU [auth A], VV [auth A], VW [auth A], VX [auth A], VY [auth A], VZ [auth A], WAA [auth A], WB [auth a], WBA [auth A], WC [auth a], WCA [auth D], 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], WT [auth A], WU [auth A], WV [auth A], WW [auth A], WX [auth A], WY [auth A], WZ [auth A], XAA [auth A], XB [auth a], XBA [auth A], XC [auth a], XCA [auth D], 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], XT [auth A], XU [auth A], XV [auth A], XW [auth A], XX [auth A], XY [auth A], XZ [auth A], YAA [auth A], YB [auth a], YBA [auth A], YC [auth a], YCA [auth D], 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], YT [auth A], YU [auth A], YV [auth A], YW [auth A], YX [auth A], YY [auth A], YZ [auth A], ZAA [auth A], ZB [auth a], ZBA [auth A], ZC [auth a], ZCA [auth D], ZD [auth a], ZE [auth a], ZF [auth n], 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], ZT [auth A], ZU [auth A], ZV [auth A], ZW [auth A], ZX [auth A], ZY [auth A], ZZ [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Rybak, M.Y., Li, L., Lin, J., Gagnon, M.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM136936
Welch Foundation	United States	H-2032-20230405
National Natural Science Foundation of China (NSFC)	China	31770784

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2024-07-31
  Changes: Data collection, Database references