2B4C

Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.319 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a V3-containing HIV-1 gp120 core.

Huang, C.C.Tang, M.Zhang, M.Y.Majeed, S.Montabana, E.Stanfield, R.L.Dimitrov, D.S.Korber, B.Sodroski, J.Wilson, I.A.Wyatt, R.Kwong, P.D.

(2005) Science 310: 1025-1028

  • DOI: 10.1126/science.1118398

  • PubMed Abstract: 
  • The third variable region (V3) of the HIV-1 gp120 envelope glycoprotein is immunodominant and contains features essential for coreceptor binding. We determined the structure of V3 in the context of an HIV-1 gp120 core complexed to the CD4 receptor an ...

    The third variable region (V3) of the HIV-1 gp120 envelope glycoprotein is immunodominant and contains features essential for coreceptor binding. We determined the structure of V3 in the context of an HIV-1 gp120 core complexed to the CD4 receptor and to the X5 antibody at 3.5 angstrom resolution. Binding of gp120 to cell-surface CD4 would position V3 so that its coreceptor-binding tip protrudes 30 angstroms from the core toward the target cell membrane. The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
envelope glycoprotein
G
344Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q75760 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q75760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD4
C
181Homo sapiensMutation(s): 0 
Gene Names: CD4
Find proteins for P01730 (Homo sapiens)
Go to Gene View: CD4
Go to UniProtKB:  P01730
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
anti-HIV-1 gp120 immunoglobulin X5 light chain
L
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
anti-HIV-1 gp120 immunoglobulin X5 heavy chain
H
235N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
G, H, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
G
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
XYL
Query on XYL

Download SDF File 
Download CCD File 
H
D-XYLITOL
C5 H12 O5
HEBKCHPVOIAQTA-SCDXWVJYSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
G
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.319 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 225.993α = 90.00
b = 225.993β = 90.00
c = 97.968γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-16
    Type: Refinement description, Source and taxonomy