4XMP

Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with HIV-1 clade A strain Q842.d12 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7831 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.

Wu, X.Zhang, Z.Schramm, C.A.Joyce, M.G.Do Kwon, Y.Zhou, T.Sheng, Z.Zhang, B.O'Dell, S.McKee, K.Georgiev, I.S.Chuang, G.Y.Longo, N.S.Lynch, R.M.Saunders, K.O.Soto, C.Srivatsan, S.Yang, Y.Bailer, R.T.Louder, M.K.Mullikin, J.C.Connors, M.Kwong, P.D.Mascola, J.R.Shapiro, L.

(2015) Cell 161: 470-485

  • DOI: 10.1016/j.cell.2015.03.004
  • Primary Citation of Related Structures:  4S1Q, 4S1R, 4S1S, 4XNY, 4XNZ, 4XVS, 4XVT

  • PubMed Abstract: 
  • HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here, we characterize the rate of maturation and extent of diversity for the ...

    HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of the study period, VRC01-lineage clades showed continuous evolution, with rates of ∼2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160
G
354Human immunodeficiency virus 1Gene Names: env
Find proteins for Q8JDI3 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q8JDI3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEAVY CHAIN OF ANTIBODY VRC08
H
235Homo sapiensGene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LIGHT CHAIN OF ANTIBODY VRC08
L
211Homo sapiensGene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Go to UniProtKB:  P01834
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
G
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7831 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.713α = 90.00
b = 82.496β = 90.00
c = 163.066γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references