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Yorodumi- EMDB-0776: Structure of the African swine fever virus major capsid protein p72 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0776 | |||||||||
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Title | Structure of the African swine fever virus major capsid protein p72 | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Keywords | capsid protein / VIRAL PROTEIN | |||||||||
Function / homology | Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / viral capsid / structural molecule activity / B646L Function and homology information | |||||||||
Biological species | African swine fever virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.67 Å | |||||||||
Authors | Liu Q / Xiang Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2019 Title: Structure of the African swine fever virus major capsid protein p72. Authors: Qi Liu / Bingting Ma / Nianchao Qian / Fan Zhang / Xu Tan / Jianlin Lei / Ye Xiang / | |||||||||
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_0776.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-0776-v30.xml emd-0776.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0776_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_0776.png | 77.8 KB | ||
Masks | emd_0776_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-0776.cif.gz | 5.7 KB | ||
Others | emd_0776_additional.map.gz emd_0776_additional_1.map.gz emd_0776_half_map_1.map.gz emd_0776_half_map_2.map.gz | 40.6 MB 40.6 MB 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0776 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0776 | HTTPS FTP |
-Related structure data
Related structure data | 6ku9MC M: atomic model generated by this map C: citing same article (ref.) |
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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_0776.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0776_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_0776_additional.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_0776_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_0776_half_map_1.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_0776_half_map_2.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : p72
Entire | Name: p72 |
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Components |
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-Supramolecule #1: p72
Supramolecule | Name: p72 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: African swine fever virus |
Molecular weight | Theoretical: 730 KDa |
-Macromolecule #1: B646L
Macromolecule | Name: B646L / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: African swine fever virus |
Molecular weight | Theoretical: 78.930531 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MHHHHHHHHH HGSDYKDHDG DYKDHDIDYK DDDDKELENL YFQGAGSMAS GGAFCLIAND GKADKIILAQ DLLNSRISNI KNVNKSYGK PDPEPTLSQI EETHLVHFNA HFKPYVPVGF EYNKVRPHTG TPTLGNKLTF GIPQYGDFFH DMVGHHILGA C HSSWQDAP ...String: MHHHHHHHHH HGSDYKDHDG DYKDHDIDYK DDDDKELENL YFQGAGSMAS GGAFCLIAND GKADKIILAQ DLLNSRISNI KNVNKSYGK PDPEPTLSQI EETHLVHFNA HFKPYVPVGF EYNKVRPHTG TPTLGNKLTF GIPQYGDFFH DMVGHHILGA C HSSWQDAP IQGTSQMGAH GQLQTFPRNG YDWDNQTPLE GAVYTLVDPF GRPIVPGTKN AYRNLVYYCE YPGERLYENV RF DVNGNSL DEYSSDVTTL VRKFCIPGDK MTGYKHLVGQ EVSVEGTSGP LLCNIHDLHK PHQSKPILTD ENDTQRTCSH TNP KFLSQH FPENSHNIQT AGKQDITPIT DATYLDIRRN VHYSCNGPQT PKYYQPPLAL WIKLRFWFNE NVNLAIPSVS IPFG ERFIT IKLASQKDLV NEFPGLFVRQ SRFIAGRPSR RNIRFKPWFI PGVINEISLT NNELYINNLF VTPEIHNLFV KRVRF SLIR VHKTQVTHTN NNHHDEKLMS ALKWPIEYMF IGLKPTWNIS DQNPHQHRDW HKFGHVVNAI MQPTHHAEIS FQDRDT ALP DACSSISDIS PVTYPITLPI IKNISVTAHG INLIDKFPSK FCSSYIPFHY GGNAIKTPDD PGAMMITFAL KPREEYQ PS GHINVSRARE FYISWDTDYV GSITTADLVV SASAINFLLL QNGSAVLRYS T UniProtKB: B646L |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot 4.5s. |
Details | GraFix sample |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-6ku9: |