5U3O

Crystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MPER Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.761 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  5U3J, 5U3K, 5U3L, 5U3M, 5U3N, 5U3P

  • 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

    Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DH511.2_K3 Fab Heavy Chain
H
235N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DH511.2_K3 Fab Light Chain
L
216N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
gp41 MPER peptide
A
20Human immunodeficiency virus type 1 group M subtype B (strain 89.6)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: 1.761 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.161 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 62.721α = 90.00
b = 101.857β = 90.00
c = 176.411γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description