+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8240 | ||||||||||||
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Title | EBOV GP in complex with IgG c2G4 and c13C6 Fabs | ||||||||||||
Map data | EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6 | ||||||||||||
Sample |
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Function / homology | Function and homology information 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 Similarity search - Function | ||||||||||||
Biological species | Zaire ebolavirus / Zaire ebolavirus (strain Mayinga-76) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||
Authors | Pallesen J / Murin CD / de Val N / Cottrell CA / Hastie KM / Turner HL / Fusco ML / Flyak AI / Zeitlin L / Crowe Jr JE ...Pallesen J / Murin CD / de Val N / Cottrell CA / Hastie KM / Turner HL / Fusco ML / Flyak AI / Zeitlin L / Crowe Jr JE / Andersen KG / Saphire EO / Ward AB | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Microbiol / Year: 2016 Title: Structures of Ebola virus GP and sGP in complex with therapeutic antibodies. Authors: Jesper Pallesen / Charles D Murin / Natalia de Val / Christopher A Cottrell / Kathryn M Hastie / Hannah L Turner / Marnie L Fusco / Andrew I Flyak / Larry Zeitlin / James E Crowe / Kristian ...Authors: Jesper Pallesen / Charles D Murin / Natalia de Val / Christopher A Cottrell / Kathryn M Hastie / Hannah L Turner / Marnie L Fusco / Andrew I Flyak / Larry Zeitlin / James E Crowe / Kristian G Andersen / Erica Ollmann Saphire / Andrew B Ward / Abstract: The Ebola virus (EBOV) GP gene encodes two glycoproteins. The major product is a soluble, dimeric glycoprotein (sGP) that is secreted abundantly. Despite the abundance of sGP during infection, little ...The Ebola virus (EBOV) GP gene encodes two glycoproteins. The major product is a soluble, dimeric glycoprotein (sGP) that is secreted abundantly. Despite the abundance of sGP during infection, little is known regarding its structure or functional role. A minor product, resulting from transcriptional editing, is the transmembrane-anchored, trimeric viral surface glycoprotein (GP). GP mediates attachment to and entry into host cells, and is the intended target of antibody therapeutics. Because large portions of sequence are shared between GP and sGP, it has been hypothesized that sGP may potentially subvert the immune response or may contribute to pathogenicity. In this study, we present cryo-electron microscopy structures of GP and sGP in complex with GP-specific and GP/sGP cross-reactive antibodies undergoing human clinical trials. The structure of the sGP dimer presented here, in complex with both an sGP-specific antibody and a GP/sGP cross-reactive antibody, permits us to unambiguously assign the oligomeric arrangement of sGP and compare its structure and epitope presentation to those of GP. We also provide biophysical evaluation of naturally occurring GP/sGP mutations that fall within the footprints identified by our high-resolution structures. Taken together, our data provide a detailed and more complete picture of the accessible Ebolavirus glycoprotein landscape and a structural basis to evaluate patient and vaccine antibody responses towards differently structured products of the GP gene. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8240.map.gz | 51.6 MB | EMDB map data format | |
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Header (meta data) | emd-8240-v30.xml emd-8240.xml | 28.5 KB 28.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8240_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_8240.png | 151.1 KB | ||
Others | emd_8240_additional_1.map.gz emd_8240_additional_2.map.gz emd_8240_additional_3.map.gz | 42.8 MB 42.8 MB 50.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8240 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8240 | HTTPS FTP |
-Validation report
Summary document | emd_8240_validation.pdf.gz | 498.7 KB | Display | EMDB validaton report |
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Full document | emd_8240_full_validation.pdf.gz | 498.2 KB | Display | |
Data in XML | emd_8240_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_8240_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8240 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8240 | HTTPS FTP |
-Related structure data
Related structure data | 5kelMC 8241C 8242C 5kemC 5kenC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8240.map.gz / Format: CCP4 / Size: 55.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6
File | emd_8240_additional_1.map | ||||||||||||
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Annotation | EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6
File | emd_8240_additional_2.map | ||||||||||||
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Annotation | EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6
File | emd_8240_additional_3.map | ||||||||||||
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Annotation | EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ebola virus trimeric surface glycoprotein in complex with IgG c2G...
Entire | Name: Ebola virus trimeric surface glycoprotein in complex with IgG c2G4 and c13C6 Fabs |
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Components |
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-Supramolecule #1: Ebola virus trimeric surface glycoprotein in complex with IgG c2G...
Supramolecule | Name: Ebola virus trimeric surface glycoprotein in complex with IgG c2G4 and c13C6 Fabs type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Zaire ebolavirus / Strain: Mayinga-76 |
Molecular weight | Experimental: 540 KDa |
-Macromolecule #1: Ebola surface glycoprotein, GP1
Macromolecule | Name: Ebola surface glycoprotein, GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 |
Molecular weight | Theoretical: 50.974031 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: IPLGVIHNST LQVSDVDKLV CRDKLSSTNQ LRSVGLNLEG NGVATDVPSA TKRWGFRSGV PPKVVNYEAG EWAENCYNLE IKKPDGSEC LPAAPDGIRG FPRCRYVHKV SGTGPCAGDF AFHKEGAFFL YDRLASTVIY RGTTFAEGVV AFLILPQAKK D FFSSHPLR ...String: IPLGVIHNST LQVSDVDKLV CRDKLSSTNQ LRSVGLNLEG NGVATDVPSA TKRWGFRSGV PPKVVNYEAG EWAENCYNLE IKKPDGSEC LPAAPDGIRG FPRCRYVHKV SGTGPCAGDF AFHKEGAFFL YDRLASTVIY RGTTFAEGVV AFLILPQAKK D FFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GK LIWKVNP EIDTTIGEWA FWETKKNLTR KIRSEELSFT VVSNGAKNIS GQSPARTSSD PGTNTTTEDH KIMASENSSA MVQ VHSQGR EAAVSHLTTL ATISTSPQSL TTKPGPDNST HNTPVYKLDI SEATQVEQHH RRTDNDSTAS DTPSATTAAG PPKA ENTNT SKSTDFLDPA TTTSPQNHSE TAGNNNTHHQ DTGEESASSG KLGLITNTIA GVAGLITGGR RTRR |
-Macromolecule #2: Ebola surface glycoprotein, GP2
Macromolecule | Name: Ebola surface glycoprotein, GP2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Zaire ebolavirus / Strain: Mayinga-76 |
Molecular weight | Theoretical: 16.137119 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: EAIVNAQPKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYTEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDKTLPDLEV DDDD |
-Macromolecule #3: c2G4 variable Fab domain heavy chain
Macromolecule | Name: c2G4 variable Fab domain heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.573105 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: EVQLQESGGG LMQPGGSMKL SCVASGFTFS NYWMNWVRQS PEKGLEWVAE IRLKSNNYAT HYAESVKGRF TISRDDSKRS VYLQMNTLR AEDTGIYYCT RGNGNYRAMD YWGQGTSVTV S |
-Macromolecule #4: c2G4 variable Fab domain light chain
Macromolecule | Name: c2G4 variable Fab domain light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.641884 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: DIQMTQSPAS LSVSVGETVS ITCRASENIY SSLAWYQQKQ GKSPQLLVYS ATILADGVPS RFSGSGSGTQ YSLKINSLQS EDFGTYYCQ HFWGTPYTFG GGTKLEIK |
-Macromolecule #5: c13C6 variable Fab domain heavy chain
Macromolecule | Name: c13C6 variable Fab domain heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.169679 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: DVKLLESGGG LVQPGGSLKL SCAASGFSLS TSGVGVGWFR QPSGKGLEWL ALIWWDDDKY YNPSLKSQLS ISKDFSRNQV FLKISNVDI ADTATYYCAR RDPFGYDNAM GYWGQGTSVT VS |
-Macromolecule #6: c13C6 variable Fab domain light chain
Macromolecule | Name: c13C6 variable Fab domain light chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.611877 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: DIVMTQSPLS LSTSVGDRVS LTCKASQNVG TAVAWYQQKP GQSPKLLIYS ASNRYTGVPD RFTGSGSGTD FTLTISNMQS EDLADYFCQ QYSSYPLTFG AGTKLELR |
-Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.4 / Component - Name: 1xTBS |
Grid | Model: C-flat-2/2 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.0093 kPa |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K / Max: 77.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 2526 / Average exposure time: 10.0 sec. / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Model building and refinement were conducted using a combination of software programs. The refinement target was optimizing using the MolProbity score while maintaining a high (good) EMRinger score. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: EMRinger |
Output model | PDB-5kel: |