4JAN

crystal structure of broadly neutralizing antibody CH103 in complex with HIV-1 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.

Liao, H.X.Lynch, R.Zhou, T.Gao, F.Alam, S.M.Boyd, S.D.Fire, A.Z.Roskin, K.M.Schramm, C.A.Zhang, Z.Zhu, J.Shapiro, L.Mullikin, J.C.Gnanakaran, S.Hraber, P.Wiehe, K.Kelsoe, G.Yang, G.Xia, S.M.Montefiori, D.C.Parks, R.Lloyd, K.E.Scearce, R.M.Soderberg, K.A.Cohen, M.Kamanga, G.Louder, M.K.Tran, L.M.Chen, Y.Cai, F.Chen, S.Moquin, S.Du, X.Joyce, M.G.Srivatsan, S.Zhang, B.Zheng, A.Shaw, G.M.Hahn, B.H.Kepler, T.B.Korber, B.T.Kwong, P.D.Mascola, J.R.Haynes, B.F.

(2013) Nature 496: 469-476

  • DOI: 10.1038/nature12053
  • Primary Citation of Related Structures:  4JAM

  • PubMed Abstract: 
  • Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details of their generation could pr ...

    Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details of their generation could provide a blueprint for effective vaccination. Here we report the isolation, evolution and structure of a broadly neutralizing antibody from an African donor followed from the time of infection. The mature antibody, CH103, neutralized approximately 55% of HIV-1 isolates, and its co-crystal structure with the HIV-1 envelope protein gp120 revealed a new loop-based mechanism of CD4-binding-site recognition. Virus and antibody gene sequencing revealed concomitant virus evolution and antibody maturation. Notably, the unmutated common ancestor of the CH103 lineage avidly bound the transmitted/founder HIV-1 envelope glycoprotein, and evolution of antibody neutralization breadth was preceded by extensive viral diversification in and near the CH103 epitope. These data determine the viral and antibody evolution leading to induction of a lineage of HIV-1 broadly neutralizing antibodies, and provide insights into strategies to elicit similar antibodies by vaccination.


    Organizational Affiliation

    Duke University Human Vaccine Institute, Departments of Medicine and Immunology, Duke University School of Medicine, Durham, North Carolina 27710, USA. hliao@duke.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
G, I
355Human immunodeficiency virus 1N/A
Find proteins for R4GRV3 (Human immunodeficiency virus 1)
Go to UniProtKB:  R4GRV3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN of CH103
H, A
226N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN of CH103
L, B
209N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H, L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
G, I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.943α = 90.00
b = 208.651β = 107.21
c = 69.422γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
SERGUIdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references
  • Version 1.2: 2013-05-01
    Type: Database references
  • Version 1.3: 2013-05-29
    Type: Database references
  • Version 1.4: 2014-07-16
    Type: Other