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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10124 | |||||||||
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Title | Structure of ZEBOV GP in complex with 5T0180 antibody | |||||||||
![]() | Locally Filtered - Z flipped | |||||||||
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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-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane ...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-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
![]() | Diskin R / Cohen-Dvashi H | |||||||||
![]() | ![]() Title: Structural Basis for a Convergent Immune Response against Ebola Virus. Authors: Hadas Cohen-Dvashi / Matthias Zehner / Stefanie Ehrhardt / Michael Katz / Nadav Elad / Florian Klein / Ron Diskin / ![]() ![]() Abstract: Ebola virus disease is a severe health problem in Africa. Vaccines that display the Zaire ebolavirus glycoprotein spike complex are a prime component for the effort to combat it. The V3-15/V1-40- ...Ebola virus disease is a severe health problem in Africa. Vaccines that display the Zaire ebolavirus glycoprotein spike complex are a prime component for the effort to combat it. The V3-15/V1-40-based class of antibodies was recently discovered to be a common response in individuals who received the Ebola virus vaccines. These antibodies display attractive properties, and thus likely contribute to the efficacy of the vaccines. Here, we use cryo-EM to elucidate how three V3-15/V1-40 antibodies from different individuals target the virus and found a convergent mechanism against a partially conserved site on the spike complex. Our study rationalizes the selection of the V3-15/V1-40 germline genes for specifically targeting this site and highlights Ebolavirus species-specific sequence divergences that may restrict breadth of V3-15/V1-40-based humoral response. The results from this study could help develop improved immunization schemes and further enable the design of immunogens that would be efficacious against a broader set of Ebolavirus species. | |||||||||
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 | ![]() | 4.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.4 KB 20.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 149.1 KB | ||
Others | ![]() ![]() | 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 433.1 KB | Display | ![]() |
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Full document | ![]() | 432.2 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s8jMC ![]() 6s8dC ![]() 6s8iC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Locally Filtered - Z flipped | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.849 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 B
File | emd_10124_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_10124_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : EBOV-GP in complex with 3T0265 antibody
Entire | Name: EBOV-GP in complex with 3T0265 antibody |
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Components |
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-Supramolecule #1: EBOV-GP in complex with 3T0265 antibody
Supramolecule | Name: EBOV-GP in complex with 3T0265 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: 5T0180 antibody
Supramolecule | Name: 5T0180 antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 / Details: A fab portion generated by cleavage |
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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: 23.130488 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYDVQWYQQ LPGTAPKVLI YGNNNRPSGV PDRFSGSKSG SSASLAITGL QAEDEADYY CQTYDSRLRD QWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT ...String: QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYDVQWYQQ LPGTAPKVLI YGNNNRPSGV PDRFSGSKSG SSASLAITGL QAEDEADYY CQTYDSRLRD QWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT TPSKQSNNKY AASSYLSLTP EQWKSHRSYS CQVTHEGSTV EKTVAPTECS |
-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: 24.636709 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: EVQLVESGGG LVKPGGSLRL SCAASGFSFG NAWMNWVRQA PGKGLEWVGR IKSKSDGGTT DYAAPVKDRF IISRDDSKKT LYLQMNSLR REDTAVYYCV RGPFYCDTCG PNDYWGQGTL VTVSSGSTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String: EVQLVESGGG LVKPGGSLRL SCAASGFSFG NAWMNWVRQA PGKGLEWVGR IKSKSDGGTT DYAAPVKDRF IISRDDSKKT LYLQMNSLR REDTAVYYCV RGPFYCDTCG PNDYWGQGTL VTVSSGSTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKRVEPKSCD KTH |
-Macromolecule #3: Envelope Glycoprotein 1
Macromolecule | Name: Envelope Glycoprotein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 35.706977 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: ETGRSIPLGV IHNSALQVSD VDKLVCRDKL SSTNQLRSVG LNLEGNGVAT DVPSATKRWG FRSGVPPKVV NYEAGEWAEN CYNLEIKKP DGSECLPAAP DGIRGFPRCR YVHKVSGTGP CAGDFAFHKE GAFFLYDRLA STVIYRGTTF AEGVVAFLIL P QAKKDFFS ...String: ETGRSIPLGV IHNSALQVSD VDKLVCRDKL SSTNQLRSVG LNLEGNGVAT DVPSATKRWG FRSGVPPKVV NYEAGEWAEN CYNLEIKKP DGSECLPAAP DGIRGFPRCR YVHKVSGTGP CAGDFAFHKE GAFFLYDRLA STVIYRGTTF AEGVVAFLIL P QAKKDFFS SHPLREPVNA TEDPSSGYYS TTIRYQATGF GTNETEYLFE VDNLTYVQLE SRFTPQFLLQ LNETIYTSGK RS NTTGKLI WKVNPEIDTT IGEWAFWETK KNLTRKIRSE ELSFTVVSTH HQDTGEESAS SGKLGLITNT IAGVAGLITG GRR TRR |
-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: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 163 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-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 / Chamber humidity: 100 % |
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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 |