4OLZ

Crystal structure of antibody VRC07-G54W in complex with clade A/E 93TH057 HIV-1 gp120 core

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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This is version 1.4 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
  • Primary Citation of Related Structures:  
    4OLU, 4OLV, 4OLW, 4OLX, 4OLY, 4OLZ, 4OM0, 4OM1

  • 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 would prevent HIV-1 transmission in humans ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A [auth G]353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env, pol
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ED31
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen binding fragment of heavy chain: Antibody VRC01B [auth H]228Homo sapiensMutation(s): 0 
Gene Names: Heavy chain
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen binding fragment of light chain: Antibody VRC01C [auth L]210Homo sapiensMutation(s): 0 
Gene Names: Light chain
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Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.911α = 90
b = 75.581β = 90
c = 198.398γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2021-06-02
    Changes: Source and taxonomy, Structure summary