5UIX

Crystal Structure of the DH576 CD4bs Fab (unliganded) from the RV305 HIV Vaccine Trial

  • Classification: IMMUNE SYSTEM
  • Expression System: Homo sapiens

  • Deposited: 2017-01-15 Released: 2017-03-08 
  • Deposition Author(s): Fera, D., Harrison, S.C.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases; Bill & Melinda Gates Foundation 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial.

Easterhoff, D.Moody, M.A.Fera, D.Cheng, H.Ackerman, M.Wiehe, K.Saunders, K.O.Pollara, J.Vandergrift, N.Parks, R.Kim, J.Michael, N.L.O'Connell, R.J.Excler, J.L.Robb, M.L.Vasan, S.Rerks-Ngarm, S.Kaewkungwal, J.Pitisuttithum, P.Nitayaphan, S.Sinangil, F.Tartaglia, J.Phogat, S.Kepler, T.B.Alam, S.M.Liao, H.X.Ferrari, G.Seaman, M.S.Montefiori, D.C.Tomaras, G.D.Harrison, S.C.Haynes, B.F.

(2017) PLoS Pathog. 13: e1006182-e1006182

  • DOI: 10.1371/journal.ppat.1006182

  • PubMed Abstract: 
  • The canary pox vector and gp120 vaccine (ALVAC-HIV and AIDSVAX B/E gp120) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy. Although the vaccine Env AE.A244 gp120 is antigenic for the unmutated common ancestor of V1V2 broa ...

    The canary pox vector and gp120 vaccine (ALVAC-HIV and AIDSVAX B/E gp120) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy. Although the vaccine Env AE.A244 gp120 is antigenic for the unmutated common ancestor of V1V2 broadly neutralizing antibody (bnAbs), no plasma bnAb activity was induced. The RV305 (NCT01435135) HIV-1 clinical trial was a placebo-controlled randomized double-blinded study that assessed the safety and efficacy of vaccine boosting on B cell repertoires. HIV-1-uninfected RV144 vaccine recipients were reimmunized 6-8 years later with AIDSVAX B/E gp120 alone, ALVAC-HIV alone, or a combination of ALVAC-HIV and AIDSVAX B/E gp120 in the RV305 trial. Env-specific post-RV144 and RV305 boost memory B cell VH mutation frequencies increased from 2.9% post-RV144 to 6.7% post-RV305. The vaccine was well tolerated with no adverse events reports. While post-boost plasma did not have bnAb activity, the vaccine boosts expanded a pool of envelope CD4 binding site (bs)-reactive memory B cells with long third heavy chain complementarity determining regions (HCDR3) whose germline precursors and affinity matured B cell clonal lineage members neutralized the HIV-1 CRF01 AE tier 2 (difficult to neutralize) primary isolate, CNE8. Electron microscopy of two of these antibodies bound with near-native gp140 trimers showed that they recognized an open conformation of the Env trimer. Although late boosting of RV144 vaccinees expanded a novel pool of neutralizing B cell clonal lineages, we hypothesize that boosts with stably closed trimers would be necessary to elicit antibodies with greater breadth of tier 2 HIV-1 strains.


    Organizational Affiliation

    Duke University, Durham, North Carolina, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DH576 Fab heavy chain
H
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DH576 Fab light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 87.638α = 90.00
b = 149.725β = 90.00
c = 74.108γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States1F32AI116355-01
Bill & Melinda Gates FoundationUnited StatesOPP1033098

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Refinement description