5U15

Crystal Structure of DH270.UCA3 (unliganded) from the DH270 Broadly Neutralizing N332-glycan Dependent Lineage

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2016-11-27 Released: 2017-03-15 
  • Deposition Author(s): Fera, D., Harrison, S.C.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.

Bonsignori, M.Kreider, E.F.Fera, D.Meyerhoff, R.R.Bradley, T.Wiehe, K.Alam, S.M.Aussedat, B.Walkowicz, W.E.Hwang, K.K.Saunders, K.O.Zhang, R.Gladden, M.A.Monroe, A.Kumar, A.Xia, S.M.Cooper, M.Louder, M.K.McKee, K.Bailer, R.T.Pier, B.W.Jette, C.A.Kelsoe, G.Williams, W.B.Morris, L.Kappes, J.Wagh, K.Kamanga, G.Cohen, M.S.Hraber, P.T.Montefiori, D.C.Trama, A.Liao, H.X.Kepler, T.B.Moody, M.A.Gao, F.Danishefsky, S.J.Mascola, J.R.Shaw, G.M.Hahn, B.H.Harrison, S.C.Korber, B.T.Haynes, B.F.

(2017) Sci Transl Med 9

  • DOI: https://doi.org/10.1126/scitranslmed.aai7514
  • Primary Citation of Related Structures:  
    5TPL, 5TPP, 5TQA, 5TRP, 5U0R, 5U0U, 5U15

  • PubMed Abstract: 

    A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs.


  • Organizational Affiliation

    Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA. mattia.bonsignori@dm.duke.edu btk@lanl.gov barton.haynes@dm.duke.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DH270.UCA3 heavy chainA,
C [auth H]
238Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH270.UCA3 light chainB,
D [auth L]
216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.533α = 90
b = 76.884β = 101.87
c = 137.097γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1F32AI116355-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM-1- AI100645

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary