5CAY

Envelope glycoprotein gp120 core from HIV type 2 bound to the first two domains of human soluble CD4 receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of an HIV-2 gp120 in Complex with CD4.

Davenport, Y.W.West, A.P.Bjorkman, P.J.

(2015) J Virol 90: 2112-2118

  • DOI: 10.1128/JVI.02678-15
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • HIV-2 is a nonpandemic form of the virus causing AIDS, and the majority of HIV-2-infected patients exhibit long-term nonprogression. The HIV-1 and HIV-2 envelope glycoproteins, the sole targets of neutralizing antibodies, share 30 to 40% identity. As ...

    HIV-2 is a nonpandemic form of the virus causing AIDS, and the majority of HIV-2-infected patients exhibit long-term nonprogression. The HIV-1 and HIV-2 envelope glycoproteins, the sole targets of neutralizing antibodies, share 30 to 40% identity. As a first step in understanding the reduced pathogenicity of HIV-2, we solved a 3.0-Å structure of an HIV-2 gp120 bound to the host receptor CD4, which reveals structural similarity to HIV-1 gp120 despite divergence in amino acid sequence.


    Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA bjorkman@caltech.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp120 core from ST strain of HIV-2
G
345Human immunodeficiency virus type 2 (ISOLATE ST)Mutation(s): 0 
Gene Names: env
Find proteins for P20872 (Human immunodeficiency virus type 2 subtype A (isolate ST))
Go to UniProtKB:  P20872
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD4
B
190Homo sapiensMutation(s): 0 
Gene Names: CD4
Find proteins for P01730 (Homo sapiens)
Go to UniProtKB:  P01730
NIH Common Fund Data Resources
PHAROS  P01730
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.276α = 90
b = 100.223β = 90
c = 199.139γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United States8 DP1 DA035082-03
Bill & Melinda Gates FoundationUnited StatesOPP1040753

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence