4TKP

Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

RING Dimerization Links Higher-Order Assembly of TRIM5 alpha to Synthesis of K63-Linked Polyubiquitin.

Yudina, Z.Roa, A.Johnson, R.Biris, N.de Souza Aranha Vieira, D.A.Tsiperson, V.Reszka, N.Taylor, A.B.Hart, P.J.Demeler, B.Diaz-Griffero, F.Ivanov, D.N.

(2015) Cell Rep 12: 788-797

  • DOI: 10.1016/j.celrep.2015.06.072
  • Primary Citation of Related Structures:  
    4TKP

  • PubMed Abstract: 
  • Members of the tripartite motif (TRIM) protein family of RING E3 ubiquitin (Ub) ligases promote innate immune responses by catalyzing synthesis of polyubiquitin chains linked through lysine 63 (K63). Here, we investigate the mechanism by which the TRIM5α ...

    Members of the tripartite motif (TRIM) protein family of RING E3 ubiquitin (Ub) ligases promote innate immune responses by catalyzing synthesis of polyubiquitin chains linked through lysine 63 (K63). Here, we investigate the mechanism by which the TRIM5α retroviral restriction factor activates Ubc13, the K63-linkage-specific E2. Structural, biochemical, and functional characterization of the TRIM5α:Ubc13-Ub interactions reveals that activation of the Ubc13-Ub conjugate requires dimerization of the TRIM5α RING domain. Our data explain how higher-order oligomerization of TRIM5α, which is promoted by the interaction with the retroviral capsid, enhances the E3 Ub ligase activity of TRIM5α and contributes to its antiretroviral function. This E3 mechanism, in which RING dimerization is transient and depends on the interaction of the TRIM protein with the ligand, is likely to be conserved in many members of the TRIM family and may have evolved to facilitate recognition of repetitive epitope patterns associated with infection.


    Organizational Affiliation

    Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA. Electronic address: ivanov@uthscsa.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 N A153Homo sapiensMutation(s): 0 
Gene Names: UBE2NBLU
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS:  P61088
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tripartite motif-containing protein 5 B93Macaca mulattaMutation(s): 0 
Gene Names: TRIM5
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q0PF16 (Macaca mulatta)
Explore Q0PF16 
Go to UniProtKB:  Q0PF16
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.17α = 90
b = 78.17β = 90
c = 82.562γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.2: 2020-03-04
    Changes: Database references