4LST

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 clade C strain ZM176.66 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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This is version 1.4 of the entry. See complete history


Literature

Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies.

Zhou, T.Zhu, J.Wu, X.Moquin, S.Zhang, B.Acharya, P.Georgiev, I.S.Altae-Tran, H.R.Chuang, G.Y.Joyce, M.G.Do Kwon, Y.Longo, N.S.Louder, M.K.Luongo, T.McKee, K.Schramm, C.A.Skinner, J.Yang, Y.Yang, Z.Zhang, Z.Zheng, A.Bonsignori, M.Haynes, B.F.Scheid, J.F.Nussenzweig, M.C.Simek, M.Burton, D.R.Koff, W.C.Mullikin, J.C.Connors, M.Shapiro, L.Nabel, G.J.Mascola, J.R.Kwong, P.D.

(2013) Immunity 39: 245-258

  • DOI: 10.1016/j.immuni.2013.04.012
  • Primary Citation of Related Structures:  
    4LSS, 4LST, 4LSU, 4LSV, 4LSP, 4LSQ, 4LSR

  • PubMed Abstract: 
  • Antibodies of the VRC01 class neutralize HIV-1, arise in diverse HIV-1-infected donors, and are potential templates for an effective HIV-1 vaccine. However, the stochastic processes that generate repertoires in each individual of >10(12) antibodies make elicitation of specific antibodies uncertain ...

    Antibodies of the VRC01 class neutralize HIV-1, arise in diverse HIV-1-infected donors, and are potential templates for an effective HIV-1 vaccine. However, the stochastic processes that generate repertoires in each individual of >10(12) antibodies make elicitation of specific antibodies uncertain. Here we determine the ontogeny of the VRC01 class by crystallography and next-generation sequencing. Despite antibody-sequence differences exceeding 50%, antibody-gp120 cocrystal structures reveal VRC01-class recognition to be remarkably similar. B cell transcripts indicate that VRC01-class antibodies require few specific genetic elements, suggesting that naive-B cells with VRC01-class features are generated regularly by recombination. Virtually all of these fail to mature, however, with only a few-likely one-ancestor B cell expanding to form a VRC01-class lineage in each donor. Developmental similarities in multiple donors thus reveal the generation of VRC01-class antibodies to be reproducible in principle, thereby providing a framework for attempts to elicit similar antibodies in the general population.


    Organizational Affiliation

    Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade CA [auth G]355Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for R4GRV3 (Human immunodeficiency virus 1)
Explore R4GRV3 
Go to UniProtKB:  R4GRV3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN OF ANTIBODY VRC01B [auth H]224Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT CHAIN OF ANTIBODY VRC01C [auth L]210Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.105α = 90
b = 77.981β = 90
c = 200.351γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2013-09-25
    Changes: Database references
  • Version 1.3: 2014-05-07
    Changes: Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary