5HJ3

Crystal structure of host-primed Ebola virus GP, GPcl.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies.

Bornholdt, Z.A.Ndungo, E.Fusco, M.L.Bale, S.Flyak, A.I.Crowe, J.E.Chandran, K.Saphire, E.O.

(2016) Mbio 7: e02154-e02115

  • DOI: 10.1128/mBio.02154-15

  • PubMed Abstract: 
  • The filovirus surface glycoprotein (GP) mediates viral entry into host cells. Following viral internalization into endosomes, GP is cleaved by host cysteine proteases to expose a receptor-binding site (RBS) that is otherwise hidden from immune survei ...

    The filovirus surface glycoprotein (GP) mediates viral entry into host cells. Following viral internalization into endosomes, GP is cleaved by host cysteine proteases to expose a receptor-binding site (RBS) that is otherwise hidden from immune surveillance. Here, we present the crystal structure of proteolytically cleaved Ebola virus GP to a resolution of 3.3 Å. We use this structure in conjunction with functional analysis of a large panel of pseudotyped viruses bearing mutant GP proteins to map the Ebola virus GP endosomal RBS at molecular resolution. Our studies indicate that binding of GP to its endosomal receptor Niemann-Pick C1 occurs in two distinct stages: the initial electrostatic interactions are followed by specific interactions with a hydrophobic trough that is exposed on the endosomally cleaved GP1 subunit. Finally, we demonstrate that monoclonal antibodies targeting the filovirus RBS neutralize all known filovirus GPs, making this conserved pocket a promising target for the development of panfilovirus therapeutics.


    Organizational Affiliation

    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA Vanderbilt Vaccine Center, Vanderbilt University, Nashville, Tennessee, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA kartik.chandran@einstein.yu.edu erica@scripps.edu.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA kartik.chandran@einstein.yu.edu erica@scripps.edu.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
C, G, K, O
179Zaire 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: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
D, H, L, P
136Zaire ebolavirus (strain Kikwit-95)Mutation(s): 0 
Gene Names: GP
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Go to UniProtKB:  P87666
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
KZ52 Antibody Fragment
E, I, M, A
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
KZ52 Antibody Fragment
F, J, N, B
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 193.103α = 90.00
b = 193.103β = 90.00
c = 350.320γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references