3SE9

Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with HIV-1 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1126/science.1207532
  • Primary Citation of Related Structures:  
    3SE8, 3SE9

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Clade AE strain 93TH057 gp120A [auth G]353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gp120
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus type 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ED31
Glycosylation
Glycosylation Sites: 10
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of antibody VRC-PG04B [auth H]228Homo sapiensMutation(s): 0 
Gene Names: antibody VRC-PG04 heavy chain
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of antibody VRC-PG04C [auth L]208Homo sapiensMutation(s): 0 
Gene Names: antibody VRC-PG04 light chain
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 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]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
IA [auth H]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
JA [auth L],
KA [auth L],
N [auth G],
O [auth G],
P [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
Q [auth G],
R [auth G],
S [auth G],
T [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BU3
Query on BU3

Download Ideal Coordinates CCD File 
DA [auth G](R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
CA [auth G]
EA [auth H]
FA [auth H]
AA [auth G],
BA [auth G],
CA [auth G],
EA [auth H],
FA [auth H],
GA [auth H],
HA [auth H],
LA [auth L],
MA [auth L],
NA [auth L],
OA [auth L],
PA [auth L],
U [auth G],
V [auth G],
W [auth G],
X [auth G],
Y [auth G],
Z [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.804α = 90
b = 66.476β = 90
c = 237.305γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-10-05
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2021-04-07
    Changes: Source and taxonomy, Structure summary
  • Version 1.4: 2024-11-27
    Changes: Data collection, Database references, Structure summary