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Yorodumi- EMDB-17312: In situ cryoEM structure of the Prototype Foamy Virus capsid, ico... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17312 | |||||||||
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Title | In situ cryoEM structure of the Prototype Foamy Virus capsid, icosahedral map | |||||||||
Map data | ||||||||||
Sample |
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Keywords | capsid / Gag / foamy virus / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Eastern chimpanzee simian foamy virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.89 Å | |||||||||
Authors | Calcraft T / Nans A / Rosenthal PB | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: In situ cryoEM structures of PFV Authors: Calcraft T / Lindemann D / Rosenthal PB | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17312.map.gz | 1.8 GB | EMDB map data format | |
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Header (meta data) | emd-17312-v30.xml emd-17312.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17312_fsc.xml | 28.2 KB | Display | FSC data file |
Images | emd_17312.png | 106.5 KB | ||
Masks | emd_17312_msk_1.map | 1.9 GB | Mask map | |
Filedesc metadata | emd-17312.cif.gz | 6 KB | ||
Others | emd_17312_half_map_1.map.gz emd_17312_half_map_2.map.gz | 1.7 GB 1.8 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17312 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17312 | HTTPS FTP |
-Validation report
Summary document | emd_17312_validation.pdf.gz | 1.4 MB | Display | EMDB validaton report |
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Full document | emd_17312_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | emd_17312_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | emd_17312_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17312 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17312 | HTTPS FTP |
-Related structure data
Related structure data | 8ozkMC 17309 17311 17313 17314 17315 17316 17317 17318 17319 17320 17321 17322 8ozhC 8ozjC 8ozlC 8ozmC 8oznC 8ozpC 8ozqC 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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-Map
File | Download / File: emd_17312.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17312_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Eastern chimpanzee simian foamy virus
Entire | Name: Eastern chimpanzee simian foamy virus |
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Components |
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-Supramolecule #1: Eastern chimpanzee simian foamy virus
Supramolecule | Name: Eastern chimpanzee simian foamy virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2170195 / Sci species name: Eastern chimpanzee simian foamy virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Virus shell | Shell ID: 1 / T number (triangulation number): 13 |
-Macromolecule #1: Gag polyprotein
Macromolecule | Name: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern chimpanzee simian foamy virus |
Molecular weight | Theoretical: 70.693414 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER FQMVRLILQN DDNEPLQRPR YEVIQRAVNP HTMFMISGP LAELQLAFQD LDLPEGPLRF GPLANGHYVQ GDPYSSSYRP VTMAETAQMT RDELEDVLNT QSEIEIQMIN L LELYEVET ...String: MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER FQMVRLILQN DDNEPLQRPR YEVIQRAVNP HTMFMISGP LAELQLAFQD LDLPEGPLRF GPLANGHYVQ GDPYSSSYRP VTMAETAQMT RDELEDVLNT QSEIEIQMIN L LELYEVET RALRRQLAER SSTGQGGISP GAPRSRPPVS SFSGLPSLPS IPGIHPRAPS PPRATSTPGN IPWSLGDDNP PS SSFPGPS QPRVSFHPGN PFVEEEGHRP RSQSRERRRE ILPAPVPSAP PMIQYIPVPP PPPIGTVIPI QHIRSVTGEP PRN PREIPI WLGRNAPAID GVFPVTTPDL RCRIINAILG GNIGLSLTPG DCLTWDSAVA TLFIRTHGTF PMHQLGNVIK GIVD QEGVA TAYTLGMMLS GQNYQLVSGI IRGYLPGQAV VTALQQRLDQ EIDDQTRAET FIQHLNAVYE ILGLNARGQS IRASV TPQP RPSRGRGRGQ NTSRPSQGPA NSGRGRQRPA SGQSNRGSST QNQNQDNLNQ GGYNLRPRTY QPQRYGGGRG RRWNDN TNN QESRPSDQGS QTPRPNQAGS GVRGNQSQTP RPAAGRGGRG NHNRNQRSSG AGDSRAVNTV TQSATSSTDE SSSAVTA AS GGDQRD UniProtKB: Gag polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
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: RECIPROCAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8ozk: |