3U36

Crystal Structure of PG9 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.281 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 

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
PG9 Fab heavy chain
H, A, C, E
248N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PG9 Fab light chain
L, B, D, F
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, D, F, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.281 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 71.594α = 107.23
b = 81.038β = 90.13
c = 91.691γ = 107.96
Software Package:
Software NamePurpose
SERGUIdata collection
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-21
    Type: Database references