3IDX

Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C222


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1126/science.1175868
  • Primary Citation of Related Structures:  
    3HI1, 3IDX, 3IDY

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 HxBc2 gp120 coreA [auth G]317Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04578 
Go to UniProtKB:  P04578
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04578
Glycosylation
Glycosylation Sites: 16
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab b13 heavy chainB [auth H]231Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab b13 light chainC [auth L]215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
T [auth G],
Z [auth H]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG
Query on NAG

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D [auth G]
E [auth G]
F [auth G]
G
H [auth G]
D [auth G],
E [auth G],
F [auth G],
G,
H [auth G],
I [auth G],
J [auth G],
K [auth G],
L [auth G],
M [auth G],
N [auth G],
O [auth G],
P [auth G],
Q [auth G],
R [auth G],
S [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

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U [auth G],
V [auth G],
W [auth G],
X [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
Y [auth G]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.609α = 90
b = 203.964β = 90
c = 109.291γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2021-03-31
    Changes: Source and taxonomy, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description