Skip to main content

 7KFG | pdb_00007kfg

Antibody Fab BDBV-289


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7KFG

This is version 1.2 of the entry. See complete history. 

Literature

Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies.

Murin, C.D., Gilchuk, P., Ilinykh, P.A., Huang, K., Kuzmina, N., Shen, X., Bruhn, J.F., Bryan, A.L., Davidson, E., Doranz, B.J., Williamson, L.E., Copps, J., Alkutkar, T., Flyak, A.I., Bukreyev, A., Crowe Jr., J.E., Ward, A.B.

(2021) Cell Rep 35: 108984-108984

  • DOI: https://doi.org/10.1016/j.celrep.2021.108984
  • Primary Citation Related Structures: 
    7KEJ, 7KEW, 7KEX, 7KF9, 7KFB, 7KFE, 7KFG, 7KFH

  • PubMed Abstract: 

    Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood. Here, we present cryoelectron microscopy (cryo-EM) structures of diverse glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLDs) to the glycan cap, which we call the MLD anchor and cradle. Antibodies that bind to the MLD cradle share common features, including use of IGHV1-69 and IGHJ6 germline genes, which exploit hydrophobic residues and form β-hairpin structures to mimic the MLD anchor, disrupt MLD attachment, destabilize GP quaternary structure, and block cleavage events required for receptor binding. Our results provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies.


  • Organizational Affiliation: 
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 47.72 kDa 
  • Atom Count: 3,270 
  • Modeled Residue Count: 434 
  • Deposited Residue Count: 446 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody Fab BDBV-289 heavy chain232Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Antibody Fab BDBV-289 light chain214Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
C [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.46α = 90
b = 94.46β = 90
c = 94.911γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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 StatesU19 AI109762
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary