+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12270 | |||||||||
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Title | Cryo-EM structure of Pepper cryptic virus 1 VLP | |||||||||
Map data | Cryo-EM structure of PCV-1 VLP. | |||||||||
Sample |
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Keywords | Partitivirus / Virus like particle / Capsid | |||||||||
Function / homology | viral capsid / membrane => GO:0016020 / Coat protein Function and homology information | |||||||||
Biological species | Pepper cryptic virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Byrne MJ / Sainsbury F | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: Structure of Pepper Cryptic Virus 1 VLP Authors: Byrne MJ / Sainsbury F / Ranson NA / Kashyap A / Esquirol L | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12270.map.gz | 469.2 MB | EMDB map data format | |
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Header (meta data) | emd-12270-v30.xml emd-12270.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12270_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_12270.png | 223 KB | ||
Filedesc metadata | emd-12270.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12270 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12270 | HTTPS FTP |
-Validation report
Summary document | emd_12270_validation.pdf.gz | 710.4 KB | Display | EMDB validaton report |
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Full document | emd_12270_full_validation.pdf.gz | 710 KB | Display | |
Data in XML | emd_12270_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_12270_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12270 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12270 | HTTPS FTP |
-Related structure data
Related structure data | 7ncrMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12270.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of PCV-1 VLP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pepper cryptic virus 1
Entire | Name: Pepper cryptic virus 1 |
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Components |
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-Supramolecule #1: Pepper cryptic virus 1
Supramolecule | Name: Pepper cryptic virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 369643 / Sci species name: Pepper cryptic virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Coat protein
Macromolecule | Name: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Pepper cryptic virus 1 |
Molecular weight | Theoretical: 47.626285 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: MGDRVNAQDD DTVVPHQAPL QPAALQQDLT RSADYLLDNV RIGNHRQRYD KYRRYVLLRS SEIFTSLVAI YAHIFSSYWQ HFRRFTDQF QAPTGVQLPT FVARVYISTW LHDLYCSIRE ATRSISPLAF NERYSYELLP YSTEYDPFLA FLSMSIKPTH I QHTPENTL ...String: MGDRVNAQDD DTVVPHQAPL QPAALQQDLT RSADYLLDNV RIGNHRQRYD KYRRYVLLRS SEIFTSLVAI YAHIFSSYWQ HFRRFTDQF QAPTGVQLPT FVARVYISTW LHDLYCSIRE ATRSISPLAF NERYSYELLP YSTEYDPFLA FLSMSIKPTH I QHTPENTL WIPILCENYD WDRNEANHNP FGITNFTLNS NLFYGLLAIL KERKEFKLST LTTNTIGRPC WLFDWHDNVQ VC AWFPREA NFNSQDVTAA YIIGVACTPK LGPSDDDAWK YYASLNSVPT FTPTEPRLTN RRSYGAYEVR TRETENNYFL PDS LLNIIE DFTATGTTQR RKIRRPSATS ASTGAAIIIR DTPGTASTAT TSTTETEVTF PPVIRTKIRD WYYHSRVILE LEDN SRTAA LRMFIIA UniProtKB: Coat protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 Details: 20 mM MOPS, pH 7.0 with 140 mM NaCl and 5% (v/v) glycerol |
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / 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 / Average electron dose: 1.12 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |