5EWI

Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody Isolated from Donor N90


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5996 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  5VGJ

  • 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
VRC38.01 Heavy Chain
H
236N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VRC38.01 Light Chain
L
220N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5996 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 62.353α = 90.00
b = 84.775β = 90.00
c = 90.003γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-05-24
    Type: Database references
  • Version 1.2: 2017-05-31
    Type: Database references