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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10003 | |||||||||
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Title | CryoEM structure of wild-type Turnip Yellows Virus | |||||||||
![]() | sharpened map | |||||||||
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Function / homology | Potato leaf roll virus readthrough protein / Potato leaf roll virus readthrough protein / Luteovirus group 1 coat protein / Luteovirus coat protein / host cell plasmodesma / host cell periplasmic space / viral capsid / structural molecule activity / Readthrough protein P3-RTD![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.08 Å | |||||||||
![]() | Trapani S / Lai Kee Him J / Hoh F / Brault V / Bron P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM structure of Turnip Yellows Virus Authors: Trapani S / Lai Kee Him J / Boissinot S / Reinbold C / Fallet C / Ancelin A / Lecorre F / Hoh F / Ziegler-Graff V / Brault V / Bron P | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 196.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.1 KB 17.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.5 KB | Display | ![]() |
Images | ![]() | 247.5 KB | ||
Others | ![]() ![]() ![]() ![]() | 163.3 MB 163.3 MB 165.8 MB 165.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 394.9 KB | Display | ![]() |
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Full document | ![]() | 394 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9fhpM M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.225 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: unsharpened map
File | emd_10003_additional.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_10003_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half 1 map
File | emd_10003_half_map_1.map | ||||||||||||
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Annotation | half_1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half 2 map
File | emd_10003_half_map_2.map | ||||||||||||
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Annotation | half_2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Beet western yellows virus-FL1
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Beet western yellows virus-FL1
Supramolecule | Name: Beet western yellows virus-FL1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12043 / Sci species name: Beet western yellows virus-FL1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Virus shell | Shell ID: 1 / Name: capsid / T number (triangulation number): 3 |
-Macromolecule #1: Major coat protein
Macromolecule | Name: Major coat protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVF SKDNLAGSSS GAITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS S QNSGSIAY ELDPHCKLNS LSSTINKFGI TKPGKRAFTA SYINGTEWHD ...String: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVF SKDNLAGSSS GAITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS S QNSGSIAY ELDPHCKLNS LSSTINKFGI TKPGKRAFTA SYINGTEWHD VAEDQFRILY KG NGSSSIA GSFRITIKCQ FHNPK |
-Macromolecule #2: Minor capsid protein P3-RTD
Macromolecule | Name: Minor capsid protein P3-RTD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVF SKDNLAGSSS GAITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS S QNSGSIAY ELDPHCKLNS LSSTINKFGI TKPGKRAFTA SYINGTEWHD ...String: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVF SKDNLAGSSS GAITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS S QNSGSIAY ELDPHCKLNS LSSTINKFGI TKPGKRAFTA SYINGTEWHD VAEDQFRILY KG NGSSSIA GSFRITIKCQ FHNPKYVDEE PGPSPGPSPS PQPTPQKKYR FIVYTGVPVT RIM AQSTDD AISLYDMPSQ RFRYIEDENM NWTNLDSRWY SQNSLKAIPM IIVPVPQGEW TVEI SMEGY QPTSSTTDPN KDKQDGLIAY NDDLSEGWNV GIYNNVEITN NKADNTLKYG HPDME LNGC HFNQGQCLER DGDLTCHIKT TGDNASFFVV GPAVQKQSKY NYAVSYGAWT DRMMEI GMI AIALDEQGSS GSVKTERPKR VGHSMAVSTW ETIKLPEKGN SEGYETSQRQ DSKTPPT AS GGSDTLDVEE GGLPLPVEEE IPDFVGDNPW SDLSTKNSQE EEAMSSESGL RPQLKPPG L PKPQPIRTIR NFDPTPDLVE AWRPDVNPGY SKADVAAATI IAGGSIKDGR SMIDKRNKA VLDGRKSWGS SLASSLTGGT LKASAKSEKL AKLTTSERAR YERIKRQQGS TRASEFLESL LAGEDPDSR F |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.32 mg/mL |
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Buffer | pH: 6 / Component - Concentration: 0.1 mol / L / Component - Name: citrate |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |