4HPY

Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report



Literature

Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2.

Liao, H.X.Bonsignori, M.Alam, S.M.McLellan, J.S.Tomaras, G.D.Moody, M.A.Kozink, D.M.Hwang, K.K.Chen, X.Tsao, C.Y.Liu, P.Lu, X.Parks, R.J.Montefiori, D.C.Ferrari, G.Pollara, J.Rao, M.Peachman, K.K.Santra, S.Letvin, N.L.Karasavvas, N.Yang, Z.Y.Dai, K.Pancera, M.Gorman, J.Wiehe, K.Nicely, N.I.Rerks-Ngarm, S.Nitayaphan, S.Kaewkungwal, J.Pitisuttithum, P.Tartaglia, J.Sinangil, F.Kim, J.H.Michael, N.L.Kepler, T.B.Kwong, P.D.Mascola, J.R.Nabel, G.J.Pinter, A.Zolla-Pazner, S.Haynes, B.F.

(2013) Immunity 38: 176-186

  • DOI: 10.1016/j.immuni.2012.11.011
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The RV144 HIV-1 trial of the canary pox vector (ALVAC-HIV) plus the gp120 AIDSVAX B/E vaccine demonstrated an estimated efficacy of 31%, which correlated directly with antibodies to HIV-1 envelope variable regions 1 and 2 (V1-V2). Genetic analysis of ...

    The RV144 HIV-1 trial of the canary pox vector (ALVAC-HIV) plus the gp120 AIDSVAX B/E vaccine demonstrated an estimated efficacy of 31%, which correlated directly with antibodies to HIV-1 envelope variable regions 1 and 2 (V1-V2). Genetic analysis of trial viruses revealed increased vaccine efficacy against viruses matching the vaccine strain at V2 residue 169. Here, we isolated four V2 monoclonal antibodies from RV144 vaccinees that recognize residue 169, neutralize laboratory-adapted HIV-1, and mediate killing of field-isolate HIV-1-infected CD4(+) T cells. Crystal structures of two of the V2 antibodies demonstrated that residue 169 can exist within divergent helical and loop conformations, which contrasted dramatically with the β strand conformation previously observed with a broadly neutralizing antibody PG9. Thus, RV144 vaccine-induced immune pressure appears to target a region that may be both sequence variable and structurally polymorphic. Variation may signal sites of HIV-1 envelope vulnerability, providing vaccine designers with new options.


    Organizational Affiliation

    Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA. hliao@duke.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CH59 Fab heavy chainH225Homo sapiensMutation(s): 0 
Gene Names: DKFZp686P15220
Find proteins for Q6N089 (Homo sapiens)
Explore Q6N089 
Go to UniProtKB:  Q6N089
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CH59 Fab light chainL215Homo sapiensMutation(s): 0 
Gene Names: IGL@
Find proteins for Q8N5F4 (Homo sapiens)
Explore Q8N5F4 
Go to UniProtKB:  Q8N5F4
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160P19Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for G9HS63 (Human immunodeficiency virus 1)
Explore G9HS63 
Go to UniProtKB:  G9HS63
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
L
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.888α = 90
b = 79.15β = 90
c = 127.112γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release