4JPW | pdb_00004jpw

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: 2.90 Å
  • R-Value Free: 
    0.265 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.cell.2013.03.018
  • Primary Citation Related Structures: 
    4GW4, 4JPV, 4JPW

  • 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 88.91 kDa 
  • Atom Count: 6,211 
  • Modeled Residue Count: 776 
  • Deposited Residue Count: 788 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375SA [auth G]353Human immunodeficiency virus 1Mutation(s): 0 
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HEAVY CHAIN OF ANTIBODY 12A21B [auth H]225Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LIGHT CHAIN OF ANTIBODY 12A21C [auth L]210Homo sapiensMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
N [auth G]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.265 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.975α = 90
b = 65.987β = 90
c = 213.023γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Structure summary