+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17996 | ||||||||||||||||||
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Title | Hepatitis B core protein with bound Geraniol | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | geraniol Hepatitis B core protein hyfrophobic pocket pocket factor Hepatitis B virus / VIRUS LIKE PARTICLE | ||||||||||||||||||
Function / homology | Function and homology information microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding Similarity search - Function | ||||||||||||||||||
Biological species | Hepatitis B virus ayw/France/Tiollais/1979 / Hepatitis B virus | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||
Authors | Makbul C / Khayenko V / Maric MH / Bottcher B | ||||||||||||||||||
Funding support | Germany, 5 items
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Citation | Journal: To Be Published Title: Peptide dimers aggregate Hepatitis B core proteins in live cells Authors: Khayenko V / Makbul C / Schulte C / Hemmelmann N / Bottcher B / Maric HM | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17996.map.gz | 301 MB | EMDB map data format | |
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Header (meta data) | emd-17996-v30.xml emd-17996.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17996_fsc.xml | 15.5 KB | Display | FSC data file |
Images | emd_17996.png | 259.6 KB | ||
Masks | emd_17996_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-17996.cif.gz | 6 KB | ||
Others | emd_17996_half_map_1.map.gz emd_17996_half_map_2.map.gz | 259.2 MB 259.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17996 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17996 | HTTPS FTP |
-Related structure data
Related structure data | 8pwoMC 8px3C 8px6C 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_17996.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17996_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17996_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17996_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hepatitis B virus
Entire | Name: Hepatitis B virus |
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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: #1 / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Sci species strain: ayw/France/Tiollais/1979 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 5 MDa |
Virus shell | Shell ID: 1 / Diameter: 360.0 Å / T number (triangulation number): 4 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Details: capsid has bound geraniol / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Hepatitis B virus ayw/France/Tiollais/1979 |
Molecular weight | Theoretical: 21.146217 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYV NTNMGLKFRQ LLWFHISCLT FGRETVIEYL VSFGVWIRTP PAYRPPNAPI LSTLPETTVV RRRGRSPRRR T PSPRRRRS QSPRRRRSQS RESQC UniProtKB: Capsid protein |
-Macromolecule #2: Geraniol
Macromolecule | Name: Geraniol / type: ligand / ID: 2 / Number of copies: 4 / Formula: 64Z |
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Molecular weight | Theoretical: 154.249 Da |
Chemical component information | ChemComp-64Z: |
-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: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.029 kPa Details: plasma cleaner (model PDC-002. Harrick Plasma, Ithaca, NY, USA); at medium power of the instrument |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 4875 / Average exposure time: 3.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000 |
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
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8pwo: |