6ORL

RF1 pre-accommodated 70S complex at 24 ms


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.

Fu, Z.Indrisiunaite, G.Kaledhonkar, S.Shah, B.Sun, M.Chen, B.Grassucci, R.A.Ehrenberg, M.Frank, J.

(2019) Nat Commun 10: 2579-2579

  • DOI: 10.1038/s41467-019-10608-z
  • Primary Citation of Related Structures:  
    6ORE, 6ORL, 6OSK, 6OSQ, 6OST, 6OT3, 6OUO

  • PubMed Abstract: 
  • When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away ...

    When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY, 10027, USA. jf2192@cumc.columbia.edu.



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50S ribosomal protein L3E [auth C]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L6H [auth F]175Escherichia coliMutation(s): 0 
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50S ribosomal protein L36EA [auth f]38Escherichia coliMutation(s): 0 
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30S ribosomal protein S2FA [auth g]225Escherichia coliMutation(s): 0 
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30S ribosomal protein S3GA [auth h]208Escherichia coliMutation(s): 0 
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30S ribosomal protein S4HA [auth i]205Escherichia coliMutation(s): 0 
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30S ribosomal protein S5IA [auth j]156Escherichia coliMutation(s): 0 
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30S ribosomal protein S6JA [auth k]104Escherichia coliMutation(s): 0 
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30S ribosomal protein S7KA [auth l]151Escherichia coliMutation(s): 0 
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30S ribosomal protein S15SA [auth t]88Escherichia coliMutation(s): 0 
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30S ribosomal protein S17UA [auth v]80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18VA [auth w]66Escherichia coliMutation(s): 0 
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30S ribosomal protein S19WA [auth x]83Escherichia coliMutation(s): 0 
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30S ribosomal protein S20XA [auth y]86Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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UniProt GroupP0A7U7
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21YA [auth z]70Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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UniProt GroupP68679
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
FME-PHE-PHEAB [auth H]3Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 1BB [auth A]257Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7I0 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7I0
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 1]2903Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
16S ribosomal RNAB [auth 2]1534Escherichia coli
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5S ribosomal RNAC [auth 3]120Escherichia coli
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Entity ID: 52
MoleculeChainsLengthOrganismImage
P-tRNAZA [auth 5]76Escherichia coli
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Entity ID: 55
MoleculeChainsLengthOrganismImage
mRNACB [auth 4]9Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
LM [auth f]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 1],
AD [auth 1],
AE [auth 1],
AF [auth 1],
AG [auth 1],
AC [auth 1],
AD [auth 1],
AE [auth 1],
AF [auth 1],
AG [auth 1],
AH [auth 1],
AI [auth 1],
AJ [auth 1],
AK [auth 1],
AL [auth 1],
AM [auth 2],
BC [auth 1],
BD [auth 1],
BE [auth 1],
BF [auth 1],
BG [auth 1],
BH [auth 1],
BI [auth 1],
BJ [auth 1],
BK [auth 1],
BL [auth 1],
BM [auth 3],
CC [auth 1],
CD [auth 1],
CE [auth 1],
CF [auth 1],
CG [auth 1],
CH [auth 1],
CI [auth 1],
CJ [auth 1],
CK [auth 1],
CL [auth 1],
CM [auth 3],
DB [auth 1],
DC [auth 1],
DD [auth 1],
DE [auth 1],
DF [auth 1],
DG [auth 1],
DH [auth 1],
DI [auth 1],
DJ [auth 1],
DK [auth 1],
DL [auth 1],
DM [auth 3],
EB [auth 1],
EC [auth 1],
ED [auth 1],
EE [auth 1],
EF [auth 1],
EG [auth 1],
EH [auth 1],
EI [auth 1],
EJ [auth 1],
EK [auth 1],
EL [auth 1],
EM [auth 3],
FB [auth 1],
FC [auth 1],
FD [auth 1],
FE [auth 1],
FF [auth 1],
FG [auth 1],
FH [auth 1],
FI [auth 1],
FJ [auth 1],
FK [auth 1],
FL [auth 1],
FM [auth 3],
GB [auth 1],
GC [auth 1],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 1],
GH [auth 1],
GI [auth 1],
GJ [auth 1],
GK [auth 1],
GL [auth 1],
GM [auth 3],
HB [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 1],
HH [auth 1],
HI [auth 1],
HJ [auth 1],
HK [auth 1],
HL [auth 1],
HM [auth 3],
IB [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 1],
IH [auth 1],
II [auth 1],
IJ [auth 1],
IK [auth 1],
IL [auth 1],
IM [auth 3],
JB [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JF [auth 1],
JG [auth 1],
JH [auth 1],
JI [auth 1],
JJ [auth 1],
JK [auth 1],
JL [auth 1],
JM [auth C],
KB [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KF [auth 1],
KG [auth 1],
KH [auth 1],
KI [auth 1],
KJ [auth 1],
KK [auth 1],
KL [auth 1],
KM [auth b],
LB [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LF [auth 1],
LG [auth 1],
LH [auth 1],
LI [auth 1],
LJ [auth 1],
LK [auth 1],
LL [auth 1],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 1],
MH [auth 1],
MI [auth 1],
MJ [auth 1],
MK [auth 1],
ML [auth 1],
MM [auth i],
NB [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 1],
NH [auth 1],
NI [auth 1],
NJ [auth 1],
NK [auth 1],
NL [auth 1],
OB [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth 1],
OF [auth 1],
OG [auth 1],
OH [auth 1],
OI [auth 1],
OJ [auth 1],
OK [auth 1],
OL [auth 1],
PB [auth 1],
PC [auth 1],
PD [auth 1],
PE [auth 1],
PF [auth 1],
PG [auth 1],
PH [auth 1],
PI [auth 1],
PJ [auth 1],
PK [auth 1],
PL [auth 1],
QB [auth 1],
QC [auth 1],
QD [auth 1],
QE [auth 1],
QF [auth 1],
QG [auth 1],
QH [auth 1],
QI [auth 1],
QJ [auth 1],
QK [auth 1],
QL [auth 1],
RB [auth 1],
RC [auth 1],
RD [auth 1],
RE [auth 1],
RF [auth 1],
RG [auth 1],
RH [auth 1],
RI [auth 1],
RJ [auth 1],
RK [auth 1],
RL [auth 1],
SB [auth 1],
SC [auth 1],
SD [auth 1],
SE [auth 1],
SF [auth 1],
SG [auth 1],
SH [auth 1],
SI [auth 1],
SJ [auth 1],
SK [auth 1],
SL [auth 1],
TB [auth 1],
TC [auth 1],
TD [auth 1],
TE [auth 1],
TF [auth 1],
TG [auth 1],
TH [auth 1],
TI [auth 1],
TJ [auth 1],
TK [auth 1],
TL [auth 1],
UB [auth 1],
UC [auth 1],
UD [auth 1],
UE [auth 1],
UF [auth 1],
UG [auth 1],
UH [auth 1],
UI [auth 1],
UJ [auth 1],
UK [auth 1],
UL [auth 1],
VB [auth 1],
VC [auth 1],
VD [auth 1],
VE [auth 1],
VF [auth 1],
VG [auth 1],
VH [auth 1],
VI [auth 1],
VJ [auth 1],
VK [auth 1],
VL [auth 1],
WB [auth 1],
WC [auth 1],
WD [auth 1],
WE [auth 1],
WF [auth 1],
WG [auth 1],
WH [auth 1],
WI [auth 1],
WJ [auth 1],
WK [auth 1],
WL [auth 1],
XB [auth 1],
XC [auth 1],
XD [auth 1],
XE [auth 1],
XF [auth 1],
XG [auth 1],
XH [auth 1],
XI [auth 1],
XJ [auth 1],
XK [auth 1],
XL [auth 1],
YB [auth 1],
YC [auth 1],
YD [auth 1],
YE [auth 1],
YF [auth 1],
YG [auth 1],
YH [auth 1],
YI [auth 1],
YJ [auth 1],
YK [auth 1],
YL [auth 1],
ZB [auth 1],
ZC [auth 1],
ZD [auth 1],
ZE [auth 1],
ZF [auth 1],
ZG [auth 1],
ZH [auth 1],
ZI [auth 1],
ZJ [auth 1],
ZK [auth 1],
ZL [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
PA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
FME
Query on FME
AB [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesGM55440
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29169
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other