5VA4

TRIM-Cyclophilin A B-box 2 and coiled-coil chimera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.306 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins.

Wagner, J.M.Christensen, D.E.Bhattacharya, A.Dawidziak, D.M.Roganowicz, M.D.Wan, Y.Pumroy, R.A.Demeler, B.Ivanov, D.N.Ganser-Pornillos, B.K.Sundquist, W.I.Pornillos, O.

(2018) J. Virol. 92: --

  • DOI: 10.1128/JVI.01563-17

  • PubMed Abstract: 
  • Restriction factors are intrinsic cellular defense proteins that have evolved to block microbial infections. Retroviruses such as HIV-1 are restricted by TRIM5 proteins, which recognize the viral capsid shell that surrounds, organizes, and protects t ...

    Restriction factors are intrinsic cellular defense proteins that have evolved to block microbial infections. Retroviruses such as HIV-1 are restricted by TRIM5 proteins, which recognize the viral capsid shell that surrounds, organizes, and protects the viral genome. TRIM5α uses a SPRY domain to bind capsids with low intrinsic affinity (KD >1 mM), and therefore requires higher-order assembly into a hexagonal lattice to generate sufficient avidity for productive capsid recognition. TRIMCyp, on the other hand, binds HIV-1 capsids through a cyclophilin A domain, which has a well-defined binding site and higher (KD ∼10 μM) affinity for isolated capsid subunits. It has therefore been argued that TRIMCyp proteins may have dispensed with the need for higher-order assembly to function as antiviral factors. Here, we show that, consistent with its high degree of sequence similarity with TRIM5α, the TRIMCyp B-box 2 domain shares the same ability to self-associate and facilitate assembly of a TRIMCyp hexagonal lattice that can wrap about the HIV-1 capsid. We also show that under stringent experimental conditions, TRIMCyp-mediated restriction of HIV-1 is indeed dependent on higher-order assembly. Both forms of TRIM5 therefore use the same mechanism of avidity-driven capsid pattern recognition.IMPORTANCE Rhesus macaques and owl monkeys are highly resistant to HIV-1 infection due to the activity of TRIM5 restriction factors. The rhesus macaque TRIM5α protein blocks HIV-1 through a mechanism that requires self-assembly of a hexagonal TRIM5α lattice around the invading viral core. Lattice assembly amplifies very weak interactions between the TRIM5α SPRY domain and the HIV-1 capsid. Assembly also promotes dimerization of the TRIM5α RING E3 ligase domain, resulting in synthesis of polyubiquitin chains that mediate downstream steps of restriction. In contrast to rhesus TRIM5α, the owl monkey TRIM5 homolog, TRIMCyp, binds isolated HIV-1 CA subunits more tightly through its cyclophilin A domain, and was therefore thought to act independent of higher-order assembly. Here, we show that TRIMCyp shares the assembly properties of TRIM5α and that both forms of TRIM5 use the same mechanism of hexagonal lattice formation to promote viral recognition and restriction.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIM5/cyclophilin A V4 fusion protein
A
141Aotus trivirgatusThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
This entity is chimeric
Mutation(s): 0 
Gene Names: serS
EC: 6.1.1.11
Find proteins for Q68KK2 (Aotus trivirgatus)
Go to UniProtKB:  Q68KK2
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
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.306 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.231 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 104.596α = 90.00
b = 104.596β = 90.00
c = 104.596γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM112508
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF32-GM115007

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references
  • Version 1.2: 2018-02-14
    Type: Database references