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- EMDB-17313: In situ cryoEM structure of the Prototype Foamy Virus capsid, pen... -
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Open data
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Basic information
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Title | In situ cryoEM structure of the Prototype Foamy Virus capsid, pentamer localised reconstruction | |||||||||
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![]() | capsid / Gag / foamy virus / pentamer / VIRAL PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Calcraft T / Nans A / Rosenthal PB | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 116.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 87.9 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 96.8 MB 96.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 904.2 KB | Display | ![]() |
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Full document | ![]() | 903.7 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ozlMC ![]() 17309 ![]() 17311 ![]() 17312 ![]() 17314 ![]() 17315 ![]() 17316 ![]() 17317 ![]() 17318 ![]() 17319 ![]() 17320 ![]() 17321 ![]() 17322 ![]() 8ozhC ![]() 8ozjC ![]() 8ozkC ![]() 8ozmC ![]() 8oznC ![]() 8ozpC ![]() 8ozqC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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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
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Eastern chimpanzee simian foamy virus
Entire | Name: ![]() |
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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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-Macromolecule #1: Gag polyprotein
Macromolecule | Name: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 70.693414 KDa |
Recombinant expression | Organism: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-8ozl: |