4B3N | pdb_00004b3n

Crystal structure of rhesus TRIM5alpha PRY/SPRY domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.248 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4B3N

This is version 2.1 of the entry. See complete history

Literature

Structural Insight Into HIV-1 Capsid Recognition by Rhesus Trim5Alpha

Yang, H.Ji, X.Zhao, G.Ning, J.Zhao, Q.Aiken, C.Gronenborn, A.M.Zhang, P.Xiong, Y.

(2012) Proc Natl Acad Sci U S A 109: 18372

  • DOI: https://doi.org/10.1073/pnas.1210903109
  • Primary Citation Related Structures: 
    4B3N

  • PubMed Abstract: 

    Tripartite motif protein isoform 5 alpha (TRIM5α) is a potent antiviral protein that restricts infection by HIV-1 and other retroviruses. TRIM5α recognizes the lattice of the retrovirus capsid through its B30.2 (PRY/SPRY) domain in a species-specific manner. Upon binding, TRIM5α induces premature disassembly of the viral capsid and activates the downstream innate immune response. We have determined the crystal structure of the rhesus TRIM5α PRY/SPRY domain that reveals essential features for capsid binding. Combined cryo-electron microscopy and biochemical data show that the monomeric rhesus TRIM5α PRY/SPRY, but not the human TRIM5α PRY/SPRY, can bind to HIV-1 capsid protein assemblies without causing disruption of the capsid. This suggests that the PRY/SPRY domain alone constitutes an important pattern-sensing component of TRIM5α that is capable of interacting with viral capsids of different curvatures. Our results provide molecular insights into the mechanisms of TRIM5α-mediated retroviral restriction.


  • Organizational Affiliation
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Macromolecule Content 

  • Total Structure Weight: 135.61 kDa 
  • Atom Count: 8,860 
  • Modeled Residue Count: 1,113 
  • Deposited Residue Count: 1,204 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MALTOSE-BINDING PERIPLASMIC PROTEIN, TRIPARTITE MOTIF-CONTAINING PROTEIN 5
A, B
602Escherichia coli BL21Macaca mulatta
This entity is chimeric
Mutation(s): 0 
EC: 2.3.2.27
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q0PF16 (Macaca mulatta)
Explore Q0PF16 
Go to UniProtKB:  Q0PF16
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ0PF16P0AEX9
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.248 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.837α = 90
b = 98.733β = 122.99
c = 110.332γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references
  • Version 1.2: 2012-11-28
    Changes: Database references
  • Version 1.3: 2017-03-15
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary