5VGJ

Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody Isolated from Donor N90, bound to a scaffolded WITO V1V2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.456 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop.

Cale, E.M.Gorman, J.Radakovich, N.A.Crooks, E.T.Osawa, K.Tong, T.Li, J.Nagarajan, R.Ozorowski, G.Ambrozak, D.R.Asokan, M.Bailer, R.T.Bennici, A.K.Chen, X.Doria-Rose, N.A.Druz, A.Feng, Y.Joyce, M.G.Louder, M.K.O'Dell, S.Oliver, C.Pancera, M.Connors, M.Hope, T.J.Kepler, T.B.Wyatt, R.T.Ward, A.B.Georgiev, I.S.Kwong, P.D.Mascola, J.R.Binley, J.M.

(2017) Immunity 46: 777-791.e10

  • DOI: 10.1016/j.immuni.2017.04.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Most HIV-1-specific neutralizing antibodies isolated to date exhibit unusual characteristics that complicate their elicitation. Neutralizing antibodies that target the V1V2 apex of the HIV-1 envelope (Env) trimer feature unusually long protruding loo ...

    Most HIV-1-specific neutralizing antibodies isolated to date exhibit unusual characteristics that complicate their elicitation. Neutralizing antibodies that target the V1V2 apex of the HIV-1 envelope (Env) trimer feature unusually long protruding loops, which enable them to penetrate the HIV-1 glycan shield. As antibodies with loops of requisite length are created through uncommon recombination events, an alternative mode of apex binding has been sought. Here, we isolated a lineage of Env apex-directed neutralizing antibodies, N90-VRC38.01-11, by using virus-like particles and conformationally stabilized Env trimers as B cell probes. A crystal structure of N90-VRC38.01 with a scaffolded V1V2 revealed a binding mode involving side-chain-to-side-chain interactions that reduced the distance the antibody loop must traverse the glycan shield, thereby facilitating V1V2 binding via a non-protruding loop. The N90-VRC38 lineage thus identifies a solution for V1V2-apex binding that provides a more conventional B cell pathway for vaccine design.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1FD6-V1V2-WITO
G
134Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q5G5U5 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q5G5U5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VRC38.01 Fab Heavy Chain
H
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VRC38.01 Fab Light Chain
L
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.456 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.572α = 90.00
b = 106.572β = 90.00
c = 129.857γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description