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: 10.1038/s41467-019-10608-z
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2B271Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6F175Escherichia coliMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9G149Escherichia coliMutation(s): 0 
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50S ribosomal protein L14K123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15L144Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L17N119Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L18O116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19P114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20Q117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21R103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22S110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23T94Escherichia coliMutation(s): 0 
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50S ribosomal protein L24U103Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W76Escherichia coliMutation(s): 0 
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50S ribosomal protein L28X77Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L29Y62Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30Z58Escherichia coliMutation(s): 0 
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50S ribosomal protein L31a66Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L34d46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35e64Escherichia coliMutation(s): 0 
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30S ribosomal protein S2g225Escherichia coliMutation(s): 0 
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30S ribosomal protein S3h208Escherichia coliMutation(s): 0 
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30S ribosomal protein S6k104Escherichia coliMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8m129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9n127Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10o99Escherichia coliMutation(s): 0 
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30S ribosomal protein S12q87Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14s100Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17v80Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19x83Escherichia coliMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20y86Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2A357Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13J142Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16M136Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25V94Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32b56Escherichia coliMutation(s): 0 
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50S ribosomal protein L33c52Escherichia coliMutation(s): 0 
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50S ribosomal protein L36f38Escherichia coliMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4i205Escherichia coliMutation(s): 0 
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30S ribosomal protein S5j156Escherichia coliMutation(s): 0 
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30S ribosomal protein S7l151Escherichia coliMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11p117Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13r116Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15t88Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16u82Escherichia coliMutation(s): 0 
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Entity ID: 50
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30S ribosomal protein S18w66Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21z70Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
FME-PHE-PHE63Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3C209Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4D201Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5E177Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChainsLengthOrganism
5S ribosomal RNA3120Escherichia coli

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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA12903Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNA21534Escherichia coli
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Entity ID: 4
MoleculeChainsLengthOrganism
mRNA49Escherichia coli

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Entity ID: 54
MoleculeChainsLengthOrganism
P-tRNA576Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
a, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
1, 2, 3, i
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
6L-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

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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 

  • 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