5U3N

Crystal Structure of DH511.12P Fab in Complex with HIV-1 gp41 MPER Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Potent and broad HIV-neutralizing antibodies in memory B cells and plasma.

Williams, L.D.Ofek, G.Schatzle, S.McDaniel, J.R.Lu, X.Nicely, N.I.Wu, L.Lougheed, C.S.Bradley, T.Louder, M.K.McKee, K.Bailer, R.T.O'Dell, S.Georgiev, I.S.Seaman, M.S.Parks, R.J.Marshall, D.J.Anasti, K.Yang, G.Nie, X.Tumba, N.L.Wiehe, K.Wagh, K.Korber, B.Kepler, T.B.Munir Alam, S.Morris, L.Kamanga, G.Cohen, M.S.Bonsignori, M.Xia, S.M.Montefiori, D.C.Kelsoe, G.Gao, F.Mascola, J.R.Moody, M.A.Saunders, K.O.Liao, H.X.Tomaras, G.D.Georgiou, G.Haynes, B.F.

(2017) Sci Immunol 2: --

  • DOI: 10.1126/sciimmunol.aal2200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. Antibody 10E8, reactive with the distal portion of the membrane-proximal external region (MPER) of HIV-1 gp41, is broadly neutralizing. However, the ontogeny ...

    Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. Antibody 10E8, reactive with the distal portion of the membrane-proximal external region (MPER) of HIV-1 gp41, is broadly neutralizing. However, the ontogeny of distal MPER antibodies and the relationship of memory B cell to plasma bnAbs are poorly understood. HIV-1-specific memory B cell flow sorting and proteomic identification of anti-MPER plasma antibodies from an HIV-1-infected individual were used to isolate broadly neutralizing distal MPER bnAbs of the same B cell clonal lineage. Structural analysis demonstrated that antibodies from memory B cells and plasma recognized the envelope gp41 bnAb epitope in a distinct orientation compared with other distal MPER bnAbs. The unmutated common ancestor of this distal MPER bnAb was autoreactive, suggesting lineage immune tolerance control. Construction of chimeric antibodies of memory B cell and plasma antibodies yielded a bnAb that potently neutralized most HIV-1 strains.


    Organizational Affiliation

    Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.,Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg 2131, South Africa.,Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Vanderbilt Vaccine Center and Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA. barton.haynes@dm.duke.edu gg@che.utexas.edu.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA.,Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Departments of Medicine, Epidemiology, and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.,Departments of Microbiology and Mathematics & Statistics, Boston University School of Medicine, Boston, MA 02118, USA.,University of North Carolina Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella 4013, South Africa.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. barton.haynes@dm.duke.edu gg@che.utexas.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DH511.12P Fab Heavy Chain
H
235N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DH511.12P Fab Light Chain
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
gp41 MPER peptide
A
28Human immunodeficiency virus type 1 group M subtype B (strain 89.6)Mutation(s): 0 
Gene Names: env
Find proteins for Q73372 (Human immunodeficiency virus type 1 group M subtype B (strain 89.6))
Go to UniProtKB:  Q73372
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 64.658α = 90.00
b = 102.518β = 90.00
c = 193.347γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction

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 States5UM1AII00645

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Author supporting evidence, Database references, Refinement description