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Yorodumi- EMDB-17319: In situ subtomogram average of the Prototype Foamy Virus capsid, ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17319 | |||||||||
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Title | In situ subtomogram average of the Prototype Foamy Virus capsid, wild-type Gag | |||||||||
Map data | ||||||||||
Sample |
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Keywords | capsid / Gag / foamy virus / VIRAL PROTEIN | |||||||||
Biological species | Eastern chimpanzee simian foamy virus | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 10.2 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_17319.map.gz | 772.5 MB | EMDB map data format | |
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Header (meta data) | emd-17319-v30.xml emd-17319.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17319_fsc.xml | 21.4 KB | Display | FSC data file |
Images | emd_17319.png | 89.3 KB | ||
Masks | emd_17319_msk_1.map | 824 MB | Mask map | |
Filedesc metadata | emd-17319.cif.gz | 5.4 KB | ||
Others | emd_17319_half_map_1.map.gz emd_17319_half_map_2.map.gz | 404.4 MB 404.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17319 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17319 | HTTPS FTP |
-Validation report
Summary document | emd_17319_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_17319_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_17319_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | emd_17319_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17319 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17319 | HTTPS FTP |
-Related structure data
Related structure data | 17309 17311 17312 17313 17314 17315 17316 17317 17318 17320 17321 17322 8ozhC 8ozjC 8ozkC 8ozlC 8ozmC 8oznC 8ozpC 8ozqC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17319.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17319_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 protein
Macromolecule | Name: Gag protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern chimpanzee simian foamy virus |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER FQMVRLILQN DDNEPLQRPR YEVIQRAVNP HTMFMISGPL AELQLAFQDL DLPEGPLRFG PLANGHYVQG DPYSSSYRPV TMAETAQMTR DELEDVLNTQ SEIEIQMINL LELYEVETRA ...String: MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER FQMVRLILQN DDNEPLQRPR YEVIQRAVNP HTMFMISGPL AELQLAFQDL DLPEGPLRFG PLANGHYVQG DPYSSSYRPV TMAETAQMTR DELEDVLNTQ SEIEIQMINL LELYEVETRA LRRQLAERSS TGQGGISPGA PRSRPPVSSF SGLPSLPSIP GIHPRAPSPP RATSTPGNIP WSLGDDNPPS SSFPGPSQPR VSFHPGNPFV EEEGHRPRSQ SRERRREILP APVPSAPPMI QYIPVPPPPP IGTVIPIQHI RSVTGEPPRN PREIPIWLGR NAPAIDGVFP VTTPDLRCRI INAILGGNIG LSLTPGDCLT WDSAVATLFI RTHGTFPMHQ LGNVIKGIVD QEGVATAYTL GMMLSGQNYQ LVSGIIRGYL PGQAVVTALQ QRLDQEIDDQ TRAETFIQHL NAVYEILGLN ARGQSIRASV TPQPRPSRGR GRGQNTSRPS QGPANSGRGR QRPASGQSNR GSSTQNQNQD NLNQGGYNLR PRTYQPQRYG GGRGRRWNDN TNNQESRPSD QGSQTPRPNQ AGSGVRGNQS QTPRPAAGRG GRGNHNRNQR SSGAGDSRAV NTVTQSATSS TDESSSAVTA ASGGDQRD |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
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) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 2.62 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: 4.5 µm / Nominal defocus min: 2.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |