2NY7 | pdb_00002ny7

HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing CD4-Binding-Site Antibody b12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.255 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

Structural definition of a conserved neutralization epitope on HIV-1 gp120.

Zhou, T.Xu, L.Dey, B.Hessell, A.J.Van Ryk, D.Xiang, S.H.Yang, X.Zhang, M.Y.Zwick, M.B.Arthos, J.Burton, D.R.Dimitrov, D.S.Sodroski, J.Wyatt, R.Nabel, G.J.Kwong, P.D.

(2007) Nature 445: 732-737

  • DOI: https://doi.org/10.1038/nature05580
  • Primary Citation Related Structures: 
    2NXY, 2NXZ, 2NY0, 2NY1, 2NY2, 2NY3, 2NY4, 2NY5, 2NY6, 2NY7

  • PubMed Abstract: 

    The remarkable diversity, glycosylation and conformational flexibility of the human immunodeficiency virus type 1 (HIV-1) envelope (Env), including substantial rearrangement of the gp120 glycoprotein upon binding the CD4 receptor, allow it to evade antibody-mediated neutralization. Despite this complexity, the HIV-1 Env must retain conserved determinants that mediate CD4 binding. To evaluate how these determinants might provide opportunities for antibody recognition, we created variants of gp120 stabilized in the CD4-bound state, assessed binding of CD4 and of receptor-binding-site antibodies, and determined the structure at 2.3 A resolution of the broadly neutralizing antibody b12 in complex with gp120. b12 binds to a conformationally invariant surface that overlaps a distinct subset of the CD4-binding site. This surface is involved in the metastable attachment of CD4, before the gp120 rearrangement required for stable engagement. A site of vulnerability, related to a functional requirement for efficient association with CD4, can therefore be targeted by antibody to neutralize HIV-1.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 86.62 kDa 
  • Atom Count: 6,181 
  • Modeled Residue Count: 735 
  • Deposited Residue Count: 762 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ENVELOPE GLYCOPROTEIN GP120A [auth G]317Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35961 
Go to UniProtKB:  P35961
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35961
Glycosylation
Glycosylation Sites: 13
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTIBODY b12, HEAVY CHAINB [auth H]230Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTIBODY b12, LIGHT CHAINC [auth L]215Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01834
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
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]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.255 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.955α = 90
b = 101.955β = 90
c = 298.294γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-11-20
    Changes: Structure summary