2NY5

HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T257S, V275C, S334A, S375W, Q428C, A433M) Complexed with CD4 and Antibody 17b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 2.1 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENVELOPE GLYCOPROTEIN GP120A [auth G]317Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P19551 (Human immunodeficiency virus type 1 group M subtype B (isolate MFA))
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Go to UniProtKB:  P19551
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UniProt GroupP19551
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD4B [auth C]184Homo sapiensMutation(s): 0 
Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens)
Explore P01730 
Go to UniProtKB:  P01730
GTEx:  ENSG00000010610 
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UniProt GroupP01730
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIBODY 17B, LIGHT CHAINC [auth L]214Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6P5S8 (Homo sapiens)
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Go to UniProtKB:  Q6P5S8
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UniProt GroupQ6P5S8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ANTIBODY 17B, HEAVY CHAIND [auth H]229Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseE [auth A]2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.262α = 90
b = 87.643β = 90
c = 197.334γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing

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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary