6QD7

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • 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). He ...

    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. florian.klein@uk-koeln.de.,Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne and University of Cologne, Cologne, Germany. florian.klein@uk-koeln.de.,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. florian.klein@uk-koeln.de.,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
MoleculeChainsSequence LengthOrganismDetails
Light chain
L, Z, P
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain
H, X, U
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1
A, C, E
322Zaire 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
B, D, F
168Zaire 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 
A, B, C, D, E, F
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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

Download SDF File 
Download CCD File 
B, D, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, C, E
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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