6VBP

Crystal structure of anti-HIV-1 antibody DH815 bound to gp120 V2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

HIV vaccine delayed boosting increases Env variable region 2-specific antibody effector functions.

Easterhoff, D.Pollara, J.Luo, K.Janus, B.Gohain, N.Williams, L.D.Tay, M.Z.Monroe, A.Peachman, K.Choe, M.Min, S.Lusso, P.Zhang, P.Go, E.P.Desaire, H.Bonsignori, M.Hwang, K.K.Beck, C.Kakalis, M.O'Connell, R.J.Vasan, S.Kim, J.H.Michael, N.L.Excler, J.L.Robb, M.L.Rerks-Ngarm, S.Kaewkungwal, J.Pitisuttithum, P.Nitayaphan, S.Sinangil, F.Tartaglia, J.Phogat, S.Wiehe, K.Saunders, K.O.Montefiori, D.C.Tomaras, G.D.Moody, M.A.Arthos, J.Rao, M.Joyce, M.G.Ofek, G.A.Ferrari, G.Haynes, B.F.

(2020) JCI Insight 5

  • DOI: https://doi.org/10.1172/jci.insight.131437
  • Primary Citation of Related Structures:  
    6VBO, 6VBP, 6VBQ

  • PubMed Abstract: 

    In the RV144 HIV-1 phase III trial, vaccine efficacy directly correlated with the magnitude of the variable region 2-specific (V2-specific) IgG antibody response, and in the presence of low plasma IgA levels, with the magnitude of plasma antibody-dependent cellular cytotoxicity. Reenrollment of RV144 vaccinees in the RV305 trial offered the opportunity to define the function, maturation, and persistence of vaccine-induced V2-specific and other mAb responses after boosting. We show that the RV144 vaccine regimen induced persistent V2 and other HIV-1 envelope-specific memory B cell clonal lineages that could be identified throughout the approximately 11-year vaccination period. Subsequent boosts increased somatic hypermutation, a critical requirement for antibody affinity maturation. Characterization of 22 vaccine-induced V2-specific mAbs with epitope specificities distinct from previously characterized RV144 V2-specific mAbs CH58 and CH59 found increased in vitro antibody-mediated effector functions. Thus, when inducing non-neutralizing antibodies, one method by which to improve HIV-1 vaccine efficacy may be through late boosting to diversify the V2-specific response to increase the breadth of antibody-mediated anti-HIV-1 effector functions.


  • Organizational Affiliation

    Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DH815 light chainA [auth L],
C [auth B],
E [auth D],
J [auth I]
220Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH815 heavy chainB [auth H],
D [auth A],
F [auth C],
K [auth J]
223Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160G [auth F],
H [auth E],
I [auth G],
L [auth K]
22Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for I2E6B7 (Human immunodeficiency virus 1)
Explore I2E6B7 
Go to UniProtKB:  I2E6B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI2E6B7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.903α = 90
b = 158.531β = 110.27
c = 92.646γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Currently 6VBP does not have a validation slider image.



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description