4FQQ

Crystal Structure of Germline Antibody PGT121-GL Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies.

Mouquet, H.Scharf, L.Euler, Z.Liu, Y.Eden, C.Scheid, J.F.Halper-Stromberg, A.Gnanapragasam, P.N.Spencer, D.I.Seaman, M.S.Schuitemaker, H.Feizi, T.Nussenzweig, M.C.Bjorkman, P.J.

(2012) Proc.Natl.Acad.Sci.USA 109: E3268-E3277

  • DOI: 10.1073/pnas.1217207109
  • Primary Citation of Related Structures:  4FQ1, 4FQ2, 4FQC

  • PubMed Abstract: 
  • Broadly neutralizing HIV antibodies (bNAbs) can recognize carbohydrate-dependent epitopes on gp120. In contrast to previously characterized glycan-dependent bNAbs that recognize high-mannose N-glycans, PGT121 binds complex-type N-glycans in glycan mi ...

    Broadly neutralizing HIV antibodies (bNAbs) can recognize carbohydrate-dependent epitopes on gp120. In contrast to previously characterized glycan-dependent bNAbs that recognize high-mannose N-glycans, PGT121 binds complex-type N-glycans in glycan microarrays. We isolated the B-cell clone encoding PGT121, which segregates into PGT121-like and 10-1074-like groups distinguished by sequence, binding affinity, carbohydrate recognition, and neutralizing activity. Group 10-1074 exhibits remarkable potency and breadth but no detectable binding to protein-free glycans. Crystal structures of unliganded PGT121, 10-1074, and their likely germ-line precursor reveal that differential carbohydrate recognition maps to a cleft between complementarity determining region (CDR)H2 and CDRH3. This cleft was occupied by a complex-type N-glycan in a "liganded" PGT121 structure. Swapping glycan contact residues between PGT121 and 10-1074 confirmed their importance for neutralization. Although PGT121 binds complex-type N-glycans, PGT121 recognized high-mannose-only HIV envelopes in isolation and on virions. As HIV envelopes exhibit varying proportions of high-mannose- and complex-type N-glycans, these results suggest promiscuous carbohydrate interactions, an advantageous adaptation ensuring neutralization of all viruses within a given strain.


    Organizational Affiliation

    Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10021, USA. hmouquet@rockefeller.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
L, A, C, E
215Homo sapiensGene Names: IGL@
Find proteins for Q8N355 (Homo sapiens)
Go to UniProtKB:  Q8N355
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chain
H, B, D, F
244Homo sapiensGene Names: IGH@
Find proteins for Q6GMX6 (Homo sapiens)
Go to UniProtKB:  Q6GMX6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
D, L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.934α = 90.00
b = 344.743β = 91.95
c = 55.230γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
SCALAdata scaling
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references