5TPP

Crystal Structure of DH270.5 (unliganded) from the DH270 Broadly Neutralizing N332-glycan Dependent Lineage

  • Classification: IMMUNE SYSTEM
  • Expression System: Homo sapiens

  • 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 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  5TPL, 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 i ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DH270.5 Fab heavy chain
L
216N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DH270.5 Fab light chain
H
238N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download SDF File 
Download CCD File 
H
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.114α = 90.00
b = 68.798β = 113.21
c = 59.463γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States1F32AI116355-01
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesUM-1- AI100645

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Refinement description