3TYG

Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with a glycosylated engineered gp120 outer domain with miniV3 (eODmV3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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
Envelope glycoprotein gp160
A
199HIV-1 unknown groupMutation(s): 5 
Gene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04578
Find proteins for Q75760 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q75760

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PGT128 light chain, Ig lambda-2 chain C regions
L
211Homo sapiensMutation(s): 0 
Gene Names: IGLC2
Find proteins for P0DOY2 (Homo sapiens)
Go to UniProtKB:  P0DOY2
NIH Common Fund Data Resources

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PGT128 heavy chain, Ig gamma-1 chain C region
H
239Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
NIH Common Fund Data Resources
PHAROS  P01857
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H, L
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.791α = 90
b = 73.512β = 90
c = 241.447γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 1.2: 2011-12-07
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence