4JPW

Crystal structure of broadly and potently neutralizing antibody 12a21 in complex with hiv-1 strain 93th057 gp120 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.904 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Somatic mutations of the immunoglobulin framework are generally required for broad and potent HIV-1 neutralization.

Klein, F.Diskin, R.Scheid, J.F.Gaebler, C.Mouquet, H.Georgiev, I.S.Pancera, M.Zhou, T.Incesu, R.B.Fu, B.Z.Gnanapragasam, P.N.Oliveira, T.Y.Seaman, M.S.Kwong, P.D.Bjorkman, P.J.Nussenzweig, M.C.

(2013) Cell 153: 126-138

  • DOI: 10.1016/j.cell.2013.03.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Broadly neutralizing antibodies (bNAbs) to HIV-1 can prevent infection and are therefore of great importance for HIV-1 vaccine design. Notably, bNAbs are¬†highly somatically mutated and generated by a fraction of HIV-1-infected individuals several yea ...

    Broadly neutralizing antibodies (bNAbs) to HIV-1 can prevent infection and are therefore of great importance for HIV-1 vaccine design. Notably, bNAbs are highly somatically mutated and generated by a fraction of HIV-1-infected individuals several years after infection. Antibodies typically accumulate mutations in the complementarity determining region (CDR) loops, which usually contact the antigen. The CDR loops are scaffolded by canonical framework regions (FWRs) that are both resistant to and less tolerant of mutations. Here, we report that in contrast to most antibodies, including those with limited HIV-1 neutralizing activity, most bNAbs require somatic mutations in their FWRs. Structural and functional analyses reveal that somatic mutations in FWR residues enhance breadth and potency by providing increased flexibility and/or direct antigen contact. Thus, in bNAbs, FWRs play an essential role beyond scaffolding the CDR loops and their unusual contribution to potency and breadth should be considered in HIV-1 vaccine design.


    Related Citations: 
    • Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies.
      Zhou, T.,Zhu, J.,Wu, X.,Moquin, S.,Zhang, B.,Acharya, P.,Georgiev, I.S.,Altae-Tran, H.R.,Chuang, G.Y.,Joyce, M.G.,Do Kwon, Y.,Longo, N.S.,Louder, M.K.,Luongo, T.,McKee, K.,Schramm, C.A.,Skinner, J.,Yang, Y.,Yang, Z.,Zhang, Z.,Zheng, A.,Bonsignori, M.,Haynes, B.F.,Scheid, J.F.,Nussenzweig, M.C.,Simek, M.,Burton, D.R.,Koff, W.C.,Mullikin, J.C.,Connors, M.,Shapiro, L.,Nabel, G.J.,Mascola, J.R.,Kwong, P.D.
      (2013) Immunity --: --


    Organizational Affiliation

    Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S
G
353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q0ED31
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEAVY CHAIN OF ANTIBODY 12A21
H
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LIGHT CHAIN OF ANTIBODY 12A21
L
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
G
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.904 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.975α = 90.00
b = 65.987β = 90.00
c = 213.023γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references