5TRP

Crystal Structure of the Unliganded DH270 Cooperating Lineage Member DH272

  • Classification: IMMUNE SYSTEM
  • Expression System: Homo sapiens

  • Deposited: 2016-10-27 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 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.692 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.211 

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:  

  • 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
DH272 Fab heavy chain
H
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DH272 Fab light chain
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.692 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.862α = 90.00
b = 124.502β = 90.00
c = 146.159γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
DENZOdata reduction
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling

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
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