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Yorodumi- EMDB-38899: Ebola virus glycoprotein in complex with a broadly neutralizing a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38899 | |||||||||
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Title | Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ANTIVIRAL PROTEIN | |||||||||
Function / homology | Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / extracellular region / membrane / SGP / Virion spike glycoprotein Function and homology information | |||||||||
Biological species | Henipavirus nipahense / Ebola virus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.98 Å | |||||||||
Authors | Fan PF / Yu CM / Chen W | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1 Authors: Fan PF / Yu CM / Chen W | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38899.map.gz | 108.9 MB | EMDB map data format | |
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Header (meta data) | emd-38899-v30.xml emd-38899.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38899_fsc.xml emd_38899_fsc_2.xml | 12.6 KB 12.6 KB | Display Display | FSC data file |
Images | emd_38899.png | 160.3 KB | ||
Filedesc metadata | emd-38899.cif.gz | 5.7 KB | ||
Others | emd_38899_half_map_1.map.gz emd_38899_half_map_2.map.gz | 200.1 MB 200.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38899 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38899 | HTTPS FTP |
-Validation report
Summary document | emd_38899_validation.pdf.gz | 852.4 KB | Display | EMDB validaton report |
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Full document | emd_38899_full_validation.pdf.gz | 851.9 KB | Display | |
Data in XML | emd_38899_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_38899_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38899 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38899 | HTTPS FTP |
-Related structure data
Related structure data | 8y3uMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38899.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38899_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38899_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ebola virus glycoprotein in complex with a broadly neutralizing a...
Entire | Name: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1 |
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Components |
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-Supramolecule #1: Ebola virus glycoprotein in complex with a broadly neutralizing a...
Supramolecule | Name: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Henipavirus nipahense |
-Supramolecule #2: Ebola virus glycoprotein
Supramolecule | Name: Ebola virus glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Ebola virus |
-Supramolecule #3: 2G1 Fab
Supramolecule | Name: 2G1 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: 2G1 VH
Macromolecule | Name: 2G1 VH / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.535075 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVKRGGSLRL SCVVSGYTFG GYSMHWVRQA PGKGLEWVSG ISSSSYYKYY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCARD MGYCSGGSCP NFDFWGQGTT VTVSS |
-Macromolecule #2: 2G1 VL
Macromolecule | Name: 2G1 VL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.342541 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: IQMTQSPSSL SASVGDRVTI TCRTSQSISN YLNWYQQIPG KAPKLLISTA SNLHSGVSSR FSGSGSGTHF TLTISSLQPE DFATYYCQQ SYSTPSFGQG TKVEIK |
-Macromolecule #3: Virion spike glycoprotein
Macromolecule | Name: Virion spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Ebola virus |
Molecular weight | Theoretical: 10.883393 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VIVNAQPKCN PNLHYWTTQD EGAAIGLAWI PYFGPAAEGI YTEGLMHNQD GLICGLRQLA NETTQALQLF LRATTELRTF SILNRKAID FLLQRWAA UniProtKB: Virion spike glycoprotein |
-Macromolecule #4: SGP
Macromolecule | Name: SGP / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Ebola virus |
Molecular weight | Theoretical: 16.984287 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SIPLGVIHNS TLQVSDVDKL VCRDKLSSTN QLRSVGLNLE GNGVATDVPS VTKRWGFRSG VPPKVVNYEA GEWAENCYNL EIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILAA UniProtKB: SGP |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 8926 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |