3IDY

Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C2221


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120.

Chen, L.Do Kwon, Y.Zhou, T.Wu, X.O'Dell, S.Cavacini, L.Hessell, A.J.Pancera, M.Tang, M.Xu, L.Yang, Z.Y.Zhang, M.Y.Arthos, J.Burton, D.R.Dimitrov, D.S.Nabel, G.J.Posner, M.R.Sodroski, J.Wyatt, R.Mascola, J.R.Kwong, P.D.

(2009) Science 326: 1123-1127

  • DOI: 10.1126/science.1175868
  • Primary Citation of Related Structures:  3HI1, 3IDX

  • PubMed Abstract: 
  • The site on HIV-1 gp120 that binds to the CD4 receptor is vulnerable to antibodies. However, most antibodies that interact with this site cannot neutralize HIV-1. To understand the basis of this resistance, we determined co-crystal structures for two ...

    The site on HIV-1 gp120 that binds to the CD4 receptor is vulnerable to antibodies. However, most antibodies that interact with this site cannot neutralize HIV-1. To understand the basis of this resistance, we determined co-crystal structures for two poorly neutralizing, CD4-binding site (CD4BS) antibodies, F105 and b13, in complexes with gp120. Both antibodies exhibited approach angles to gp120 similar to those of CD4 and a rare, broadly neutralizing CD4BS antibody, b12. Slight differences in recognition, however, resulted in substantial differences in F105- and b13-bound conformations relative to b12-bound gp120. Modeling and binding experiments revealed these conformations to be poorly compatible with the viral spike. This incompatibility, the consequence of slight differences in CD4BS recognition, renders HIV-1 resistant to all but the most accurately targeted antibodies.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 HxBc2 gp120 core
G, A
317Human immunodeficiency virus type 1 group M subtype BGene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04578
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab b13 heavy chain
H, B
231N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab b13 light chain
L, C
215N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 106.168α = 90.00
b = 204.316β = 90.00
c = 216.886γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance