Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer -A6B3C3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 306196.50 
• Atom Count: 14445 
• Residue Count: 2784 
• Unique protein chains: 4

6QD7

EM structure of a EBOV-GP bound to 3T0331 neutralizing antibody

• DOI: 10.2210/pdb6QD7/pdb
• EMDataResource: EMD-4520

• Classification: VIRAL PROTEIN
• Organism(s): Zaire ebolavirus (strain Mayinga-76)
• Expression System: Homo sapiens


• Deposited: 2019-01-01 Released: 2019-10-02 
• Deposition Author(s): Diskin, R., Cohen-Dvashi, H.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.1 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV.

Ehrhardt, S.A., Zehner, M., Krahling, V., Cohen-Dvashi, H., Kreer, C., Elad, N., Gruell, H., Ercanoglu, M.S., Schommers, P., Gieselmann, L., Eggeling, R., Dahlke, C., Wolf, T., Pfeifer, N., Addo, M.M., Diskin, R., Becker, S., Klein, F.

(2019) Nat. Med. 25: 1589-1600

• PubMed: 31591605 
• DOI: 10.1038/s41591-019-0602-4


• PubMed Abstract: 
  

Recombinant vesicular stomatitis virus-Zaire Ebola virus (rVSV-ZEBOV) is the most advanced Ebola virus vaccine candidate and is currently being used to combat the outbreak of Ebola virus disease (EVD) in the Democratic Republic of the Congo (DRC). Here we examine the humoral immune response in a subset of human volunteers enrolled in a phase 1 rVSV-ZEBOV vaccination trial by performing comprehensive single B cell and electron microscopy structure analyses. Four studied vaccinees show polyclonal, yet reproducible and convergent B cell responses with shared sequence characteristics. EBOV-targeting antibodies cross-react with other Ebolavirus species, and detailed epitope mapping revealed overlapping target epitopes with antibodies isolated from EVD survivors. Moreover, in all vaccinees, we detected highly potent EBOV-neutralizing antibodies with activities comparable or superior to the monoclonal antibodies currently used in clinical trials. These include antibodies combining the IGHV3-15/IGLV1-40 immunoglobulin gene segments that were identified in all investigated individuals. Our findings will help to evaluate and direct current and future vaccination strategies and offer opportunities for novel EVD therapies.

---

Organizational Affiliation: 

Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany. [e-mail].,Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne and University of Cologne, Cologne, Germany. [e-mail].,German Center for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany.,Division of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.,Institute of Virology, Faculty of Medicine, Philipps University Marburg, Marburg, Germany.,German Center for Infection Research, Partner Site Gießen-Marburg-Langen, Marburg, Germany.,Faculty of Medicine, University of Tübingen, Tübingen, Germany.,Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany. [e-mail].,Department of Infectious Diseases, University Hospital Frankfurt, Frankfurt/Main, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany.,Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Department of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Methods in Medical Informatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Light chain	L, Z, P	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Heavy chain	H, X, U	224	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1	A, C, E	322	Zaire 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
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein	B, D, F	168	Zaire 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	A, B, C, D, E, F	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	B, D, F	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	B, D, F	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	A, C, E	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.1 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-01-01 
• Released Date: 2019-10-02 
• Deposition Author(s): Diskin, R., Cohen-Dvashi, H.

Revision History 

• Version 1.0: 2019-10-02
  Type: Initial release
• Version 1.1: 2019-10-16
  Type: Data collection, Database references
• Version 1.2: 2019-10-23
  Type: Data collection, Database references
• Version 1.3: 2019-11-27
  Type: Database references