5IEA

TRIM5 B-box2 and coiled-coil chimera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.258 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5 alpha.

Wagner, J.M.Roganowicz, M.D.Skorupka, K.Alam, S.L.Christensen, D.E.Doss, G.L.Wan, Y.Frank, G.A.Ganser-Pornillos, B.K.Sundquist, W.I.Pornillos, O.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.16309
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. Mammalian TRIM5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and ac ...

    Restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. Mammalian TRIM5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and activate ubiquitin-dependent antiviral responses upon capsid recognition. Here, we report crystallographic and functional studies of the TRIM5α B-box 2 domain, which mediates higher-order assembly of TRIM5 proteins. The B-box can form both dimers and trimers, and the trimers can link multiple TRIM5α proteins into a hexagonal net that matches the lattice arrangement of capsid subunits and enables avid capsid binding. Two modes of conformational flexibility allow TRIM5α to accommodate the variable curvature of retroviral capsids. B-box mediated interactions also modulate TRIM5α's E3 ubiquitin ligase activity, by stereochemically restricting how the N-terminal RING domain can dimerize. Overall, these studies define important molecular details of cellular recognition of retroviruses, and how recognition links to downstream processes to disable the virus.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
A, B, C, D, F, K
141Macaca mulattaThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
This entity is chimeric
Mutation(s): 0 
Gene Names: TRIM5, serS
EC: 2.3.2.27 6.1.1.11
Find proteins for Q0PF16 (Macaca mulatta)
Go to Gene View: TRIM5
Go to UniProtKB:  Q0PF16
Find proteins for P34945 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P34945
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, F, K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.258 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.227α = 90.00
b = 71.486β = 90.00
c = 213.834γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations