3SE8

Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with HIV-1 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing.

Wu, X.Zhou, T.Zhu, J.Zhang, B.Georgiev, I.Wang, C.Chen, X.Longo, N.S.Louder, M.McKee, K.O'Dell, S.Perfetto, S.Schmidt, S.D.Shi, W.Wu, L.Yang, Y.Yang, Z.Y.Yang, Z.Zhang, Z.Bonsignori, M.Crump, J.A.Kapiga, S.H.Sam, N.E.Haynes, B.F.Simek, M.Burton, D.R.Koff, W.C.Doria-Rose, N.A.Connors, M.Mullikin, J.C.Nabel, G.J.Roederer, M.Shapiro, L.Kwong, P.D.Mascola, J.R.

(2011) Science 333: 1593-1602

  • DOI: 10.1126/science.1207532
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals ...

    Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.


    Organizational Affiliation

    Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Clade AE strain 93TH057 gp120G353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gp120env
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of antibody VRC03H233Homo sapiensMutation(s): 0 
Gene Names: antibody VRC03 heavy chain
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Light chain of antibody VRC03L209Homo sapiensMutation(s): 0 
Gene Names: antibody VRC03 light chain
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
G
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TRS
Query on TRS

Download CCD File 
H
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
G, H, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
H
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.01α = 90
b = 70.259β = 90
c = 217.879γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-06-10 
  • Released Date: 2011-08-10 
  • Deposition Author(s): Kwong, P.D., Zhou, T.

Revision History 

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-10-05
    Changes: Database references
  • Version 1.2: 2012-08-15
    Changes: Other
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary