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- EMDB-6888: Cryo-EM structure of HBV Cp164 capsid treated with micrococcal nu... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6888 | |||||||||
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Title | Cryo-EM structure of HBV Cp164 capsid treated with micrococcal nuclease | |||||||||
![]() | HBV Cp-164 capsid treated with micrococcal nuclease | |||||||||
![]() | HBV core protein-164 != Hepatitis B virus HBV core protein-164
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
![]() | He J / Li Z / Gao Y / Yan D / Sun J / Zhang Q / Liu S | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 228.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.8 KB 9.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16 KB | Display | ![]() |
Images | ![]() | 318.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.3 KB | Display | ![]() |
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Full document | ![]() | 77.4 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HBV Cp-164 capsid treated with micrococcal nuclease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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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: ![]() ![]() |
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: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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