6OT3

RF2 accommodated state bound Release complex 70S at 24 ms


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: https://doi.org/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. 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 Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2E [auth B]271Escherichia coliMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L3F [auth C]209Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4G [auth D]201Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5H [auth E]177Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6I [auth F]175Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9J [auth G]149Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth K]123Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15M [auth L]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16N [auth M]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17O [auth N]119Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L18P [auth O]116Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L19Q [auth P]114Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20R [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth R]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22T [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth T]94Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth U]103Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27X [auth W]76Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Y [auth X]77Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Z [auth Y]62Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth Z]58Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31BA [auth a]66Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth b]56Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33DA [auth c]52Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth d]46Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth e]64Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth f]38Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2HA [auth g]225Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3IA [auth h]208Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4JA [auth i]205Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5KA [auth j]156Escherichia coliMutation(s): 0 
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Entity ID: 38
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30S ribosomal protein S6LA [auth k]104Escherichia coliMutation(s): 0 
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30S ribosomal protein S7MA [auth l]151Escherichia coliMutation(s): 0 
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30S ribosomal protein S8NA [auth m]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9OA [auth n]127Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10PA [auth o]99Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11QA [auth p]117Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12RA [auth q]87Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13SA [auth r]116Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14TA [auth s]100Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15UA [auth t]88Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16VA [auth u]82Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17WA [auth v]80Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18XA [auth w]66Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19YA [auth x]83Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20ZA [auth y]86Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21AB [auth z]70Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 2CB [auth A]357Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
FME-PHE-PHEDB [auth 6]3Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 1]2,903Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
16S ribosomal RNAB [auth 2]1,534Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth 3]120Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
mRNAD [auth 4]9Escherichia coli
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Entity ID: 54
MoleculeChains LengthOrganismImage
P-tRNABB [auth 5]76Escherichia 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 
PB [auth a],
QB [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
EB [auth 1]
FB [auth 1]
GB [auth 2]
HB [auth 3]
IB [auth 3]
EB [auth 1],
FB [auth 1],
GB [auth 2],
HB [auth 3],
IB [auth 3],
JB [auth 3],
KB [auth 3],
LB [auth 3],
MB [auth 3],
NB [auth 3],
OB [auth 3],
RB [auth i]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
DB [auth 6]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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