3TWC

Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with Man9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield.

Pejchal, R.Doores, K.J.Walker, L.M.Khayat, R.Huang, P.S.Wang, S.K.Stanfield, R.L.Julien, J.P.Ramos, A.Crispin, M.Depetris, R.Katpally, U.Marozsan, A.Cupo, A.Maloveste, S.Liu, Y.McBride, R.Ito, Y.Sanders, R.W.Ogohara, C.Paulson, J.C.Feizi, T.Scanlan, C.N.Wong, C.H.Moore, J.P.Olson, W.C.Ward, A.B.Poignard, P.Schief, W.R.Burton, D.R.Wilson, I.A.

(2011) Science 334: 1097-1103

  • DOI: 10.1126/science.1213256
  • Primary Citation of Related Structures:  3TV3, 3TYG

  • PubMed Abstract: 
  • The HIV envelope (Env) protein gp120 is protected from antibody recognition by a dense glycan shield. However, several of the recently identified PGT broadly neutralizing antibodies appear to interact directly with the HIV glycan coat. Crystal struct ...

    The HIV envelope (Env) protein gp120 is protected from antibody recognition by a dense glycan shield. However, several of the recently identified PGT broadly neutralizing antibodies appear to interact directly with the HIV glycan coat. Crystal structures of antigen-binding fragments (Fabs) PGT 127 and 128 with Man(9) at 1.65 and 1.29 angstrom resolution, respectively, and glycan binding data delineate a specific high mannose-binding site. Fab PGT 128 complexed with a fully glycosylated gp120 outer domain at 3.25 angstroms reveals that the antibody penetrates the glycan shield and recognizes two conserved glycans as well as a short β-strand segment of the gp120 V3 loop, accounting for its high binding affinity and broad specificity. Furthermore, our data suggest that the high neutralization potency of PGT 127 and 128 immunoglobulin Gs may be mediated by cross-linking Env trimers on the viral surface.


    Organizational Affiliation

    Department of Molecular Biology, Skaggs Institute for Chemical Biology and International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, nhe Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PGT127 light chain, Ig lambda-2 chain C regions
L
211N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PGT127 heavy chain, Ig gamma-1 chain C region
H
239N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
AML
Query on AML

Download SDF File 
Download CCD File 
H
AMYLAMINE
C5 H13 N
DPBLXKKOBLCELK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H, L
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.550α = 90.00
b = 71.600β = 117.02
c = 78.830γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-10-26
    Type: Database references
  • Version 1.2: 2011-12-07
    Type: Database references
  • Version 1.3: 2017-08-02
    Type: Refinement description, Source and taxonomy