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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4520 | |||||||||
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Title | EM structure of a EBOV-GP bound to 3T0331 neutralizing antibody | |||||||||
![]() | Local filtered map | |||||||||
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Function / homology | ![]() host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Diskin R / Cohen-Dvashi H | |||||||||
![]() | ![]() Title: Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV. Authors: Stefanie A Ehrhardt / Matthias Zehner / Verena Krähling / Hadas Cohen-Dvashi / Christoph Kreer / Nadav Elad / Henning Gruell / Meryem S Ercanoglu / Philipp Schommers / Lutz Gieselmann / ...Authors: Stefanie A Ehrhardt / Matthias Zehner / Verena Krähling / Hadas Cohen-Dvashi / Christoph Kreer / Nadav Elad / Henning Gruell / Meryem S Ercanoglu / Philipp Schommers / Lutz Gieselmann / Ralf Eggeling / Christine Dahlke / Timo Wolf / Nico Pfeifer / Marylyn M Addo / Ron Diskin / Stephan Becker / Florian Klein / ![]() ![]() 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) ...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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.4 KB 21.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15 KB | Display | ![]() |
Images | ![]() | 174 KB | ||
Others | ![]() ![]() | 165.4 MB 165.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 446 KB | Display | ![]() |
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Full document | ![]() | 445.1 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qd7MC ![]() 4521C ![]() 6qd8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Local filtered map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map A
File | emd_4520_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_4520_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : EBOV-GP in complex with neutralizing 3T0331 antibody
Entire | Name: EBOV-GP in complex with neutralizing 3T0331 antibody |
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Components |
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-Supramolecule #1: EBOV-GP in complex with neutralizing 3T0331 antibody
Supramolecule | Name: EBOV-GP in complex with neutralizing 3T0331 antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: EBOV-GP
Supramolecule | Name: EBOV-GP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: neutralizing 3T0331 antibody
Supramolecule | Name: neutralizing 3T0331 antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Light chain
Macromolecule | Name: Light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.310885 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: EIVLTQSPAT LSLSPGERAT LSCRASQSVS TYLAWYQHQP GQAPRLLIYE ASNRATGIPA RFSGSGSGTE FTLTISSLEP EDVAVYYCQ QRASWPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: EIVLTQSPAT LSLSPGERAT LSCRASQSVS TYLAWYQHQP GQAPRLLIYE ASNRATGIPA RFSGSGSGTE FTLTISSLEP EDVAVYYCQ QRASWPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #2: Heavy chain
Macromolecule | Name: Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.673553 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: EVQLLESGGG LVQPGGSLRL SCEASGFPLR DYAMSWVRQA PGRGLQWVST IGGNDNAANY ADSVKGRFTV SRDNSKSTIY LQMNSLRAE DTALYFCAKS VRLSRPSPFD LWGQGSLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String: EVQLLESGGG LVQPGGSLRL SCEASGFPLR DYAMSWVRQA PGRGLQWVST IGGNDNAANY ADSVKGRFTV SRDNSKSTIY LQMNSLRAE DTALYFCAKS VRLSRPSPFD LWGQGSLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSC |
-Macromolecule #3: Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1
Macromolecule | Name: Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1 type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34.887578 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GSRSIPLGVI HNSALQVSDV DKLVCRDKLS STNQLRSVGL NLEGNGVATD VPSATKRWGF RSGVPPKVVN YEAGEWAENC YNLEIKKPD GSECLPAAPD GIRGFPRCRY VHKVSGTGPC AGDFAFHKEG AFFLYDRLAS TVIYRGTTFA EGVVAFLILP Q AKKDFFSS ...String: GSRSIPLGVI HNSALQVSDV DKLVCRDKLS STNQLRSVGL NLEGNGVATD VPSATKRWGF RSGVPPKVVN YEAGEWAENC YNLEIKKPD GSECLPAAPD GIRGFPRCRY VHKVSGTGPC AGDFAFHKEG AFFLYDRLAS TVIYRGTTFA EGVVAFLILP Q AKKDFFSS HPLREPVNAT EDPSSGYYST TIRYQATGFG TNETEYLFEV DNLTYVQLES RFTPQFLLQL NETIYTSGKR SN TTGKLIW KVNPEIDTTI GEWAFWETKK NLTRKIRSEE LSFTVV(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #4: Envelope glycoprotein
Macromolecule | Name: Envelope glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 18.989391 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: EAIVNAQPKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYIEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDGSGYIPEA PRDGQAYVRK DGEWVLLSTF L GTHHHHHH |
-Macromolecule #6: alpha-D-mannopyranose
Macromolecule | Name: alpha-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: MAN |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ![]() ChemComp-MAN: |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 27.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |