5VVF

Crystal Structure of 354BG1 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 

wwPDB Validation  3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies.

Wang, H.Gristick, H.B.Scharf, L.West, A.P.Galimidi, R.P.Seaman, M.S.Freund, N.T.Nussenzweig, M.C.Bjorkman, P.J.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.27389
  • Primary Citation of Related Structures:  5VIY, 5VJ6

  • PubMed Abstract: 
  • The HIV-1 envelope (Env) glycoprotein binds to host cell receptors to mediate membrane fusion. The prefusion Env trimer is stabilized by V1V2 loops that interact at the trimer apex. Broadly neutralizing antibodies (bNAbs) against V1V2 loops, exemplif ...

    The HIV-1 envelope (Env) glycoprotein binds to host cell receptors to mediate membrane fusion. The prefusion Env trimer is stabilized by V1V2 loops that interact at the trimer apex. Broadly neutralizing antibodies (bNAbs) against V1V2 loops, exemplified by PG9, bind asymmetrically as a single Fab to the apex of the symmetric Env trimer using a protruding CDRH3 to penetrate the Env glycan shield. Here we characterized a distinct mode of V1V2 epitope recognition by the new bNAb BG1 in which two Fabs bind asymmetrically per Env trimer using a compact CDRH3. Comparisons between cryo-EM structures of Env trimer complexed with BG1 (6.2 Å resolution) and PG9 (11.5 Å resolution) revealed a new V1V2-targeting strategy by BG1. Analyses of the EM structures provided information relevant to vaccine design including molecular details for different modes of asymmetric recognition of Env trimer and a binding model for BG1 recognition of V1V2 involving glycan flexibility.


    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
Molecule Chains Sequence Length Organism Details
354BG1 Heavy Chain
H
251 N/A N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
Molecule Chains Sequence Length Organism Details
354BG1 Light Chain
L
214 N/A N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
L
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å) Angle (°)
a = 95.630 α = 90.00
b = 95.630 β = 90.00
c = 103.951 γ = 120.00
Software Package:
Software Name Purpose
iMOSFLM data processing
PHENIX refinement
Aimless data scaling
Aimless data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding Organization Country Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases United States 5P01AI100148

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release