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Yorodumi- EMDB-6888: Cryo-EM structure of HBV Cp164 capsid treated with micrococcal nu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6888 | |||||||||
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Title | Cryo-EM structure of HBV Cp164 capsid treated with micrococcal nuclease | |||||||||
Map data | HBV Cp-164 capsid treated with micrococcal nuclease | |||||||||
Sample | HBV core protein-164 != Hepatitis B virus HBV core protein-164
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Biological species | Hepatitis B virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
Authors | He J / Li Z / Gao Y / Yan D / Sun J / Zhang Q / Liu S | |||||||||
Citation | Journal: To Be Published Title: Insights into the Structural Organization of Carboxy-Terminal Domain via Nuclease Sensitivity of Hepatitis B Virus Capsid Authors: He J / Li Z / Gao Y / Yan D / Sun J / Zhang Q / Liu S | |||||||||
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_6888.map.gz | 228.7 MB | EMDB map data format | |
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Header (meta data) | emd-6888-v30.xml emd-6888.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6888_fsc.xml | 16 KB | Display | FSC data file |
Images | emd_6888.png | 318.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6888 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6888 | HTTPS FTP |
-Validation report
Summary document | emd_6888_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_6888_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_6888_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6888 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6888 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6888.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HBV Cp-164 capsid treated with micrococcal nuclease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : HBV core protein-164
Entire | Name: HBV core protein-164 |
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Components |
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-Supramolecule #1: Hepatitis B virus
Supramolecule | Name: Hepatitis B virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host system | Organism: Escherichia coli (E. coli) |
Virus shell | Shell ID: 1 / T number (triangulation number): 4 |
-Macromolecule #1: HBV core protein-164
Macromolecule | Name: HBV core protein-164 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Hepatitis B virus |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDIDPYKEFG ASVELLSFLP SDFFPSIRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMNLAT WVGSNLEDPA SRELVVSYVN VNMGLKIRQL LWFHISCLTF GRETVLEYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVR RRGRSPRRRT PSPR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 15 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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