5TPP

Crystal Structure of DH270.5 (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: 2016-10-20 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: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1126/scitranslmed.aai7514
  • Structures With Same Primary Citation

  • 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 ...

    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

    Duke Human Vaccine Institute, Durham, NC 27710, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DH270.5 Fab heavy chainL216Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DH270.5 Fab light chainH238Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download CCD File 
H
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.114α = 90
b = 68.798β = 113.21
c = 59.463γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
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 

  • 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