4OM0

Crystal structure of antibody VRC07-G54Y in complex with clade A/E 93TH057 HIV-1 gp120 core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo.

Rudicell, R.S.Kwon, Y.D.Ko, S.Y.Pegu, A.Louder, M.K.Georgiev, I.S.Wu, X.Zhu, J.Boyington, J.C.Chen, X.Shi, W.Yang, Z.Y.Doria-Rose, N.A.McKee, K.O'Dell, S.Schmidt, S.D.Chuang, G.Y.Druz, A.Soto, C.Yang, Y.Zhang, B.Zhou, T.Todd, J.P.Lloyd, K.E.Eudailey, J.Roberts, K.E.Donald, B.R.Bailer, R.T.Ledgerwood, J.Mullikin, J.C.Shapiro, L.Koup, R.A.Graham, B.S.Nason, M.C.Connors, M.Haynes, B.F.Rao, S.S.Roederer, M.Kwong, P.D.Mascola, J.R.Nabel, G.J.

(2014) J Virol 88: 12669-12682

  • DOI: 10.1128/JVI.02213-14
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Over the past 5 years, a new generation of highly potent and broadly neutralizing HIV-1 antibodies has been identified. These antibodies can protect against lentiviral infection in nonhuman primates (NHPs), suggesting that passive antibody transfer w ...

    Over the past 5 years, a new generation of highly potent and broadly neutralizing HIV-1 antibodies has been identified. These antibodies can protect against lentiviral infection in nonhuman primates (NHPs), suggesting that passive antibody transfer would prevent HIV-1 transmission in humans. To increase the protective efficacy of such monoclonal antibodies, we employed next-generation sequencing, computational bioinformatics, and structure-guided design to enhance the neutralization potency and breadth of VRC01, an antibody that targets the CD4 binding site of the HIV-1 envelope. One variant, VRC07-523, was 5- to 8-fold more potent than VRC01, neutralized 96% of viruses tested, and displayed minimal autoreactivity. To compare its protective efficacy to that of VRC01 in vivo, we performed a series of simian-human immunodeficiency virus (SHIV) challenge experiments in nonhuman primates and calculated the doses of VRC07-523 and VRC01 that provide 50% protection (EC50). VRC07-523 prevented infection in NHPs at a 5-fold lower concentration than VRC01. These results suggest that increased neutralization potency in vitro correlates with improved protection against infection in vivo, documenting the improved functional efficacy of VRC07-523 and its potential clinical relevance for protecting against HIV-1 infection in humans.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA jmascola@nih.gov gary.nabel@sanofi.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160G353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: envpol
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antigen binding fragment of heavy chain: Antibody VRC01H228Homo sapiensMutation(s): 0 
Gene Names: Heavy chain
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Antigen binding fragment of light chain: Antibody VRC01L210Homo sapiensMutation(s): 0 
Gene Names: Light chain
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
G
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.9α = 90
b = 75.528β = 90
c = 198.292γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary