6MAM

Cleaved Ebola GP in complex with a broadly neutralizing human antibody, ADI-15946


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of broad ebolavirus neutralization by a human survivor antibody.

West, B.R.Wec, A.Z.Moyer, C.L.Fusco, M.L.Ilinykh, P.A.Huang, K.Wirchnianski, A.S.James, R.M.Herbert, A.S.Hui, S.Goodwin, E.Howell, K.A.Kailasan, S.Aman, M.J.Walker, L.M.Dye, J.M.Bukreyev, A.Chandran, K.Saphire, E.O.

(2019) Nat. Struct. Mol. Biol. 26: 204-212

  • DOI: 10.1038/s41594-019-0191-4

  • PubMed Abstract: 
  • The structural features that govern broad-spectrum activity of broadly neutralizing anti-ebolavirus antibodies (Abs) outside of the internal fusion loop epitope are currently unknown. Here we describe the structure of a broadly neutralizing human mon ...

    The structural features that govern broad-spectrum activity of broadly neutralizing anti-ebolavirus antibodies (Abs) outside of the internal fusion loop epitope are currently unknown. Here we describe the structure of a broadly neutralizing human monoclonal Ab (mAb), ADI-15946, which was identified in a human survivor of the 2013-2016 outbreak. The crystal structure of ADI-15946 in complex with cleaved Ebola virus glycoprotein (EBOV GP CL ) reveals that binding of the mAb structurally mimics the conserved interaction between the EBOV GP core and its glycan cap β17-β18 loop to inhibit infection. Both endosomal proteolysis of EBOV GP and binding of mAb FVM09 displace this loop, thereby increasing exposure of ADI-15946's conserved epitope and enhancing neutralization. Our work also mapped the paratope of ADI-15946, thereby explaining reduced activity against Sudan virus, which enabled rational, structure-guided engineering to enhance binding and neutralization of Sudan virus while retaining the parental activity against EBOV and Bundibugyo virus.


    Organizational Affiliation

    Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA.,Adimab LLC, Lebanon, NH, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA. erica@scripps.edu.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA. erica@scripps.edu.,Integrated Biotherapeutics, Rockville, MD, USA.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.,Division of Virology, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA.,Mapp Biopharmaceutical, San Diego, CA, USA.,Department of Immunology and Microbiology, University of Texas Medical Branch, Galveston, TX, USA.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA. kartik.chandran@einstein.yu.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADI-15946 Fab Heavy Chain
A, C, E
242N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ADI-15946 Fab Light Chain
B, D, F
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
G, I, K
234Zaire ebolavirus (strain Mayinga-76)Mutation(s): 0 
Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05320
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
H, J, L
110Zaire ebolavirus (strain Mayinga-76)Mutation(s): 0 
Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76))
Go to UniProtKB:  Q05320
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
H, J, L
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
H, J, L
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.262 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 182.273α = 90.00
b = 182.273β = 90.00
c = 262.012γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

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 Diseases (NIH/NIAID)United StatesU19 AI09762-04
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI132204
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19 AI109711
Defense Threat Reduction Agency (DTRA)United StatesHDTRA1-13-1-0034

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-18
    Type: Author supporting evidence