6OKQ

Crystal structure of the SF12 Fab

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2019-04-14 Released: 2019-06-05 
  • Deposition Author(s): Barnes, C.O., Bjorkman, P.J.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope.

Schoofs, T.Barnes, C.O.Suh-Toma, N.Golijanin, J.Schommers, P.Gruell, H.West Jr., A.P.Bach, F.Lee, Y.E.Nogueira, L.Georgiev, I.S.Bailer, R.T.Czartoski, J.Mascola, J.R.Seaman, M.S.McElrath, M.J.Doria-Rose, N.A.Klein, F.Nussenzweig, M.C.Bjorkman, P.J.

(2019) Immunity 50: 1513

  • DOI: https://doi.org/10.1016/j.immuni.2019.04.014
  • Primary Citation of Related Structures:  
    6OKP, 6OKQ

  • PubMed Abstract: 

    Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization breadth from an HIV-infected donor. SF12 recognized a glycan-dominated epitope on Env's silent face and was potent against clade AE viruses, which are poorly covered by V3-glycan bNAbs. A 3.3Å cryo-EM structure of a SF12-Env trimer complex showed additional contacts to Env protein residues by SF12 compared with VRC-PG05, the only other known donor-derived silentface antibody, explaining SF12's increased neutralization breadth, potency, and resistance to Env mutation routes. Asymmetric binding of SF12 was associated with distinct N-glycan conformations across Env protomers, demonstrating intra-Env glycan heterogeneity. Administrating SF12 to HIV-1-infected humanized mice suppressed viremia and selected for viruses lacking the N448 gp120 glycan. Effective bNAbs can therefore be raised against HIV-1 Env's silent face, suggesting their potential for HIV-1 prevention, therapy, and vaccine development.


  • Organizational Affiliation

    Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SF12 Fab Heavy Chain,SF12 Fab Heavy Chain
A, D, F
242Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOX5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SF12 Fab Light Chain,SF12 Fab Light Chain
B, C, E
211Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8TCD0 (Homo sapiens)
Explore Q8TCD0 
Go to UniProtKB:  Q8TCD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TCD0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.018α = 90
b = 223.018β = 90
c = 288.296γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI100148
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50 GM082545-06

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description