5FEC

Crystal structure of 3BNC60 Fab germline precursor in complex with 426c.TM4deltaV1-3 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  5F7E, 5FA2, 5I9Q, 5IGX

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
germline 3BNC60 heavy chain
H, A
230N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
germline 3BNC60 light chain
L, B
210N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
426c.TM4deltaV1-3 gp120
C, D, G, I
353Human immunodeficiency virus 1Gene Names: env
Find proteins for A0A0K1H6P9 (Human immunodeficiency virus 1)
Go to UniProtKB:  A0A0K1H6P9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
C, D, G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
C, D, G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
C, D, G, I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 103.070α = 90.00
b = 134.103β = 90.00
c = 194.955γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations