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 

wwPDB Validation   3D Report Full Report


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·ribos ...

    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.



Macromolecules

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30S ribosomal protein S2AB241Escherichia coliMutation(s): 0 
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30S ribosomal protein S3AC233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4AD206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5AE167Escherichia coliMutation(s): 0 
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30S ribosomal protein S10AJ103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11AK129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12AL124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13AM118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14AN101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15AO89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16AP82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17AQ84Escherichia coliMutation(s): 0 
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30S ribosomal protein S18AR75Escherichia coliMutation(s): 0 
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30S ribosomal protein S19AS92Escherichia coliMutation(s): 0 
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30S ribosomal protein S20AT87Escherichia coliMutation(s): 0 
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Peptide chain release factor 3AW534Escherichia coliMutation(s): 0 
Gene Names: b4375JW5873miaDprfCTermination Release Factor 3tos
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50S ribosomal protein L27B085Escherichia coliMutation(s): 0 
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50S ribosomal protein L28B178Escherichia coliMutation(s): 0 
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50S ribosomal protein L29B263Escherichia coliMutation(s): 0 
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50S ribosomal protein L30B359Escherichia coliMutation(s): 0 
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50S ribosomal protein L32B457Escherichia coliMutation(s): 0 
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50S ribosomal protein L33B555Escherichia coliMutation(s): 0 
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50S ribosomal protein L34B646Escherichia coliMutation(s): 0 
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50S ribosomal protein L35B765Escherichia coliMutation(s): 0 
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50S ribosomal protein L36B838Escherichia coliMutation(s): 0 
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50S ribosomal protein L2BC273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3BD209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4BE201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5BF179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6BG177Escherichia coliMutation(s): 0 
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50S ribosomal protein L10BH165Escherichia coliMutation(s): 0 
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50S ribosomal protein L11BI142Escherichia coliMutation(s): 0 
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50S ribosomal protein L7/L12BJBKBLBM121Escherichia coliMutation(s): 0 
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50S ribosomal protein L13BN142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14BO123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15BP144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16BQ136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17BR127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18BS117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19BT115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20BU118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21BV103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22BW110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23BX100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24BY104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25BZ94Escherichia coliMutation(s): 0 
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16S rRNAAA1533Escherichia coli
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messenger RNAAV27synthetic construct
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23S rRNABA2903Escherichia coli
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5S rRNABB118Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download CCD File 
AW
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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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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Entry History 

Deposition Data

Revision History 

  • 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