8FZD

Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with apoRF3, RF1, P- and E-site tRNAPhe (Composite state I-B)


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 

  • 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]241Escherichia coliMutation(s): 0 
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Entity ID: 3
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30S ribosomal protein S3C [auth c]233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]131Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]156Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10J [auth j]103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11K [auth k]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12L [auth l]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13M [auth m]118Escherichia coliMutation(s): 0 
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Entity ID: 14
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30S ribosomal protein S14N [auth n]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15O [auth o]89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16P [auth p]82Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]84Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]75Escherichia coliMutation(s): 0 
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Entity ID: 19
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30S ribosomal protein S19S [auth s]92Escherichia coliMutation(s): 0 
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Entity ID: 20
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30S ribosomal protein S20T [auth t]87Escherichia coliMutation(s): 0 
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Entity ID: 21
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30S ribosomal protein S21U [auth u]71Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 1Y [auth w]360Escherichia coliMutation(s): 0 
Gene Names: prfA
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor RF3Z [auth v]529Escherichia coli K-12Mutation(s): 0 
Gene Names: prfCmiaDtosb4375JW5873
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Entity ID: 29
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50S ribosomal protein L2CA [auth C]273Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L3DA [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L4EA [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L5FA [auth F]179Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L6GA [auth G]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L9HA [auth H]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L10IA [auth I]165Escherichia coliMutation(s): 0 
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50S ribosomal protein L11JA [auth J]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13KA [auth L]142Escherichia coliMutation(s): 0 
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Entity ID: 38
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50S ribosomal protein L14LA [auth M]123Escherichia coliMutation(s): 0 
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Entity ID: 39
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50S ribosomal protein L15MA [auth N]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16NA [auth O]136Escherichia coliMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L17OA [auth P]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18PA [auth Q]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19QA [auth R]115Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20RA [auth S]118Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L21SA [auth T]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22TA [auth U]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23UA [auth V]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24VA [auth W]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25WA [auth X]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27XA [auth Y]85Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28YA [auth Z]78Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29ZA [auth 1]63Escherichia coliMutation(s): 0 
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UniProt GroupP0A7M6
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AB [auth 2]59Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31BB [auth 3]70Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CB [auth 4]57Escherichia coliMutation(s): 0 
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Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33DB [auth 5]55Escherichia coliMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34EB [auth 6]46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35FB [auth 7]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36GB [auth 8]38Escherichia coliMutation(s): 0 
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Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S Ribosomal RNAA [auth a]1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-site phenylalanyl-tRNAV [auth x]76Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
P-site phenylalanyl-tRNAW [auth y]76Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
F-UAA mRNAX [auth z]21Escherichia phage T4
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Entity ID: 27
MoleculeChains LengthOrganismImage
23S Ribosomal RNAAA [auth A]2,904Escherichia coli
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Entity ID: 28
MoleculeChains LengthOrganismImage
5S Ribosomal RNABA [auth B]120Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
NX [auth 3],
RX [auth 8]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth a]
AD [auth a]
AE [auth a]
AF [auth a]
AG [auth a]
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],
AU [auth A],
AV [auth A],
AW [auth A],
AX [auth B],
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],
BU [auth A],
BV [auth A],
BW [auth A],
BX [auth B],
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],
CU [auth A],
CV [auth A],
CW [auth A],
CX [auth B],
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],
DU [auth A],
DV [auth A],
DW [auth A],
DX [auth B],
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],
EU [auth A],
EV [auth A],
EW [auth A],
EX [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],
FU [auth A],
FV [auth A],
FW [auth A],
FX [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],
GU [auth A],
GV [auth A],
GW [auth A],
GX [auth B],
HB [auth a],
HC [auth a],
HD [auth a],
HE [auth a],
HF [auth a],
HG [auth n],
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 C],
IB [auth a],
IC [auth a],
ID [auth a],
IE [auth a],
IF [auth a],
IG [auth x],
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 C],
JB [auth a],
JC [auth a],
JD [auth a],
JE [auth a],
JF [auth a],
JG [auth x],
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 N],
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 A],
KT [auth A],
KU [auth A],
KV [auth A],
KW [auth A],
KX [auth S],
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 A],
LT [auth A],
LU [auth A],
LV [auth A],
LW [auth A],
LX [auth S],
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 A],
MT [auth A],
MU [auth A],
MV [auth A],
MW [auth A],
MX [auth V],
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 A],
NT [auth A],
NU [auth A],
NV [auth A],
NW [auth A],
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 A],
OT [auth A],
OU [auth A],
OV [auth A],
OW [auth A],
OX [auth 4],
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],
PT [auth A],
PU [auth A],
PV [auth A],
PW [auth A],
PX [auth 6],
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],
QT [auth A],
QU [auth A],
QV [auth A],
QW [auth A],
QX [auth 7],
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],
RT [auth A],
RU [auth A],
RV [auth A],
RW [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],
ST [auth A],
SU [auth A],
SV [auth A],
SW [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],
TT [auth A],
TU [auth A],
TV [auth A],
TW [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],
UT [auth A],
UU [auth A],
UV [auth A],
UW [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],
VT [auth A],
VU [auth A],
VV [auth A],
VW [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],
WT [auth A],
WU [auth A],
WV [auth A],
WW [auth B],
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],
XT [auth A],
XU [auth A],
XV [auth A],
XW [auth B],
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],
YT [auth A],
YU [auth A],
YV [auth A],
YW [auth B],
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],
ZT [auth A],
ZU [auth A],
ZV [auth A],
ZW [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L [auth l]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
DA [auth D]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
NA [auth O]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM136936
Welch FoundationUnited StatesH-2032-20230405
National Natural Science Foundation of China (NSFC)China31770784

Revision History  (Full details and data files)

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