3U1S

Crystal structure of human Fab PGT145, a broadly reactive and potent HIV-1 neutralizing antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.

McLellan, J.S.Pancera, M.Carrico, C.Gorman, J.Julien, J.P.Khayat, R.Louder, R.Pejchal, R.Sastry, M.Dai, K.O'Dell, S.Patel, N.Shahzad-Ul-Hussan, S.Yang, Y.Zhang, B.Zhou, T.Zhu, J.Boyington, J.C.Chuang, G.Y.Diwanji, D.Georgiev, I.Do Kwon, Y.Lee, D.Louder, M.K.Moquin, S.Schmidt, S.D.Yang, Z.Y.Bonsignori, M.Crump, J.A.Kapiga, S.H.Sam, N.E.Haynes, B.F.Burton, D.R.Koff, W.C.Walker, L.M.Phogat, S.Wyatt, R.Orwenyo, J.Wang, L.X.Arthos, J.Bewley, C.A.Mascola, J.R.Nabel, G.J.Schief, W.R.Ward, A.B.Wilson, I.A.Kwong, P.D.

(2011) Nature 480: 336-343

  • DOI: 10.1038/nature10696
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylat ...

    Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded β-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab PGT145 Light chain
L
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab PGT145 Heavy chain
H
267N/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
SO4
Query on SO4

Download SDF File 
Download CCD File 
H, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
H
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 118.730α = 90.00
b = 118.730β = 90.00
c = 101.184γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
XDSdata reduction
Blu-Icedata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2011-12-21
    Type: Database references