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- EMDB-10001: CryoEM structure of modified Turnip Yellows Virus devoid of minor... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10001 | |||||||||
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Title | CryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain | |||||||||
![]() | Sharpened map | |||||||||
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![]() | virus | |||||||||
Function / homology | Luteovirus group 1 coat protein / Luteovirus coat protein / T=3 icosahedral viral capsid / structural molecule activity / Major capsid protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
![]() | Trapani S / Lai Kee Him J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: CryoEM structure of modified Turnip Yellows Virus devoid of minor capsid protein readthrough domain 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 | ![]() | 194.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.3 KB 16.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 264.7 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() ![]() | 164.7 MB 165.3 MB 165.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rtkMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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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_10001_additional.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half 1 map
File | emd_10001_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_10001_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 capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.52252 KDa |
Sequence | String: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVFS KDNLAGSSSG AITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS SQNSGSIAYE LDPHCKLNSL SSTINKFGIT KPGKRAFTAS Y INGTEWHD ...String: MNTVVGRRII NGRRRPRRQT RRAQRPQPVV VVQTSRATQR RPRRRRRGNN RTGRTVPTRG AGSSETFVFS KDNLAGSSSG AITFGPSLS DCPAFSNGML KAYHEYKISM VILEFVSEAS SQNSGSIAYE LDPHCKLNSL SSTINKFGIT KPGKRAFTAS Y INGTEWHD VAEDQFRILY KGNGSSSIAG SFRITIKCQF HNPK UniProtKB: Major capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-6rtk: |