4V89

Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome (without viomycin)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome.

Zhou, J.Lancaster, L.Trakhanov, S.Noller, H.F.

(2012) RNA 18: 230-240

  • DOI: 10.1261/rna.031187.111
  • Primary Citation of Related Structures:  
    4V85, 4V89

  • PubMed Abstract: 
  • The class II release factor RF3 is a GTPase related to elongation factor EF-G, which catalyzes release of class I release factors RF1 and RF2 from the ribosome after termination of protein synthesis. The 3.3 Å crystal structure of the RF3·GDPNP·ribosome complex provides a high-resolution description of interactions and structural rearrangements that occur when binding of this translational GTPase induces large-scale rotational movements in the ribosome ...

    The class II release factor RF3 is a GTPase related to elongation factor EF-G, which catalyzes release of class I release factors RF1 and RF2 from the ribosome after termination of protein synthesis. The 3.3 Å crystal structure of the RF3·GDPNP·ribosome complex provides a high-resolution description of interactions and structural rearrangements that occur when binding of this translational GTPase induces large-scale rotational movements in the ribosome. RF3 induces a 7° rotation of the body and 14° rotation of the head of the 30S ribosomal subunit, and itself undergoes inter- and intradomain conformational rearrangements. We suggest that ordering of critical elements of switch loop I and the P loop, which help to form the GTPase catalytic site, are caused by interactions between the G domain of RF3 and the sarcin-ricin loop of 23S rRNA. The rotational movements in the ribosome induced by RF3, and its distinctly different binding orientation to the sarcin-ricin loop of 23S rRNA, raise interesting implications for the mechanism of action of EF-G in translocation.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, CA 95064, USA.



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30S ribosomal protein S2B [auth AB]241Escherichia coliMutation(s): 0 
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30S ribosomal protein S14N [auth AN]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15O [auth AO]89Escherichia coliMutation(s): 0 
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Peptide chain release factor 3W [auth AW]534Escherichia coliMutation(s): 0 
Gene Names: b4375JW5873miaDprfCTermination Release Factor 3tos
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50S ribosomal protein L7/L12PA [auth BJ], QA [auth BK], RA [auth BL], SA [auth BM]121Escherichia coliMutation(s): 0 
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50S ribosomal protein L14UA [auth BO]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15VA [auth BP]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L17XA [auth BR]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L19ZA [auth BT]115Escherichia coliMutation(s): 0 
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50S ribosomal protein L21BB [auth BV]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L23DB [auth BX]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24EB [auth BY]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25FB [auth BZ]94Escherichia coliMutation(s): 0 
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16S rRNAA [auth AA]1533Escherichia coli
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messenger RNAV [auth AV]27synthetic construct
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23S rRNAGA [auth BA]2903Escherichia coli
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Entity ID: 34
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5S rRNAHA [auth BB]118Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
GB [auth AW]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
HB [auth AW]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 258α = 90
b = 312β = 90
c = 333γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
CNSrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description