4YE4

Crystal Structure of Neutralizing Antibody HJ16 in Complex with HIV-1 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.

Zhou, T.Lynch, R.M.Chen, L.Acharya, P.Wu, X.Doria-Rose, N.A.Joyce, M.G.Lingwood, D.Soto, C.Bailer, R.T.Ernandes, M.J.Kong, R.Longo, N.S.Louder, M.K.McKee, K.O'Dell, S.Schmidt, S.D.Tran, L.Yang, Z.Druz, A.Luongo, T.S.Moquin, S.Srivatsan, S.Yang, Y.Zhang, B.Zheng, A.Pancera, M.Kirys, T.Georgiev, I.S.Gindin, T.Peng, H.P.Yang, A.S.Mullikin, J.C.Gray, M.D.Stamatatos, L.Burton, D.R.Koff, W.C.Cohen, M.S.Haynes, B.F.Casazza, J.P.Connors, M.Corti, D.Lanzavecchia, A.Sattentau, Q.J.Weiss, R.A.West Jr., A.P.Bjorkman, P.J.Scheid, J.F.Nussenzweig, M.C.Shapiro, L.Mascola, J.R.Kwong, P.D.

(2015) Cell 161: 1280-1292

  • DOI: https://doi.org/10.1016/j.cell.2015.05.007
  • Primary Citation of Related Structures:  
    4RWY, 4RX4, 4YDI, 4YDJ, 4YDK, 4YDL, 4YE4, 4YFL

  • PubMed Abstract: 

    The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures -8 determined here- of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HT593.1 gp120A [auth G]356Human immunodeficiency virusMutation(s): 0 
UniProt
Find proteins for Q69994 (Human immunodeficiency virus 1)
Explore Q69994 
Go to UniProtKB:  Q69994
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ69994
Glycosylation
Glycosylation Sites: 8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain human antibody HJ16B [auth H]228Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of HJ16C [auth L]218Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.712α = 90
b = 99.037β = 90
c = 180.426γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Experimental preparation
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2020-03-04
    Changes: Data collection, Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2022-03-30
    Changes: Author supporting evidence, Database references, Structure summary