5F7E

Crystal structure of germ-line precursor of 3BNC60 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for germline antibody recognition of HIV-1 immunogens.

Scharf, L.West, A.P.Sievers, S.A.Chen, C.Jiang, S.Gao, H.Gray, M.D.McGuire, A.T.Scheid, J.F.Nussenzweig, M.C.Stamatatos, L.Bjorkman, P.J.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.13783
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Efforts to elicit broadly neutralizing antibodies (bNAbs) against HIV-1 require understanding germline bNAb recognition of HIV-1 envelope glycoprotein (Env). The VRC01-class bNAb family derived from the VH1-2*02 germline allele arose in multiple HIV- ...

    Efforts to elicit broadly neutralizing antibodies (bNAbs) against HIV-1 require understanding germline bNAb recognition of HIV-1 envelope glycoprotein (Env). The VRC01-class bNAb family derived from the VH1-2*02 germline allele arose in multiple HIV-1-infected donors, yet targets the CD4-binding site on Env with common interactions. Modified forms of the 426c Env that activate germline-reverted B cell receptors are candidate immunogens for eliciting VRC01-class bNAbs. We present structures of germline-reverted VRC01-class bNAbs alone and complexed with 426c-based gp120 immunogens. Germline bNAb-426c gp120 complexes showed preservation of VRC01-class signature residues and gp120 contacts, but detectably different binding modes compared to mature bNAb-gp120 complexes. Unlike typical antibody-antigen interactions, VRC01-class germline antibodies exhibited preformed antigen-binding conformations for recognizing immunogens. Affinity maturation introduced substitutions increasing induced-fit recognition and electropositivity, potentially to accommodate negatively-charged complex-type N-glycans on gp120. These results provide general principles relevant to the unusual evolution of VRC01-class bNAbs and guidelines for structure-based immunogen design.


    Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Laboratory of Molecular Immunology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, The Rockefeller University, New York, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chain
H
231N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
L
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.857α = 90.00
b = 74.857β = 90.00
c = 83.113γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesHIVRAD P01 AI100148
Bill & Melinda Gates FoundationUnited States1040753

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-13
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations