2GON

Xray Structure of Gag133-278


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Implications for Viral Capsid Assembly from Crystal Structures of HIV-1 Gag 1-278 and CAN 133-278.

Kelly, B.N.Howard, B.R.Wang, H.Robinson, H.Sundquist, W.I.Hill, C.P.

(2006) Biochemistry 45: 11257-11266

  • DOI: 10.1021/bi060927x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gag, the major structural protein of retroviruses such as HIV-1, comprises a series of domains connected by flexible linkers. These domains drive viral assembly by mediating multiple interactions between adjacent Gag molecules and by binding to viral ...

    Gag, the major structural protein of retroviruses such as HIV-1, comprises a series of domains connected by flexible linkers. These domains drive viral assembly by mediating multiple interactions between adjacent Gag molecules and by binding to viral genomic RNA and host cell membranes. Upon viral budding, Gag is processed by the viral protease to liberate distinct domains as separate proteins. The first two regions of Gag are MA, a membrane-binding module, and CA, which is a two-domain protein that makes important Gag-Gag interactions, forms the cone-shaped outer shell of the core (the capsid) in the mature HIV-1 particle, and makes an important interaction with the cellular protein cyclophilin A (CypA). Here, we report crystal structures of the mature CA N-terminal domain (CA(N)(133-278)) and a MA-CA(N) fusion (Gag(1-278)) at resolutions/R(free) values of 1.9 A/25.7% and 2.2 A/25.8%, respectively. Consistent with earlier studies, a comparison of these structures indicates that processing at the MA-CA junction causes CA to adopt an N-terminal beta-hairpin conformation that seems to be required for capsid morphology and viral infectivity. In contrast with an NMR study (Tang, C., et al. (2002) Nat. Struct. Biol. 9, 537-543), structural overlap reveals only small relative displacements for helix 6, which is located between the beta-hairpin and the CypA-binding loop. These observations argue against the proposal that CypA binding is coupled with beta-hairpin formation and support an earlier surface plasmon resonance study (Yoo, S., et al. (1997) J. Mol. Biol. 269, 780-795), which concluded that beta-hairpin formation and CypA-binding are energetically independent events.


    Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112-5650, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24 (CA)
A, B, C, D
146Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download SDF File 
Download CCD File 
A, D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.260α = 90.00
b = 134.509β = 90.00
c = 42.086γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
SOLVEphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-04-13 
  • Released Date: 2006-09-26 
  • Deposition Author(s): Kelly, B.N.

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance