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Yorodumi- EMDB-3565: Cowpea mosaic virus top component (CPMV-T) - naturally occurring ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3565 | |||||||||
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Title | Cowpea mosaic virus top component (CPMV-T) - naturally occurring empty particles | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CPMV-M / plant virus / picornavirales / virus | |||||||||
Function / homology | Function and homology information transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / GTP binding / structural molecule activity / DNA binding / RNA binding Similarity search - Function | |||||||||
Biological species | Cowpea mosaic virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.25 Å | |||||||||
Authors | Hesketh EL / Meshcheriakova Y | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Sci Rep / Year: 2017 Title: The structures of a naturally empty cowpea mosaic virus particle and its genome-containing counterpart by cryo-electron microscopy. Authors: Emma L Hesketh / Yulia Meshcheriakova / Rebecca F Thompson / George P Lomonossoff / Neil A Ranson / Abstract: Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. ...Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. Here, we report high resolution cryo electron microscopy (cryo-EM) maps of wild type CPMV containing RNA-2, and of naturally-formed empty CPMV capsids. The resolution of these structures is sufficient to visualise large amino acids. We have refined an atomic model for each map and identified an essential amino acid involved in genome encapsidation. This work has furthered our knowledge of Picornavirales genome encapsidation and will assist further work in the development of CPMV as a biotechnological tool. | |||||||||
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_3565.map.gz | 45.8 MB | EMDB map data format | |
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Header (meta data) | emd-3565-v30.xml emd-3565.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3565_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_3565.png | 267.2 KB | ||
Filedesc metadata | emd-3565.cif.gz | 5.8 KB | ||
Others | emd_3565_additional.map.gz | 165.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3565 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3565 | HTTPS FTP |
-Validation report
Summary document | emd_3565_validation.pdf.gz | 575.5 KB | Display | EMDB validaton report |
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Full document | emd_3565_full_validation.pdf.gz | 575 KB | Display | |
Data in XML | emd_3565_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_3565_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3565 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3565 | HTTPS FTP |
-Related structure data
Related structure data | 5mshMC 3562C 8609C 5ms1C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3565.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 3565 additional.map
File | emd_3565_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cowpea mosaic virus
Entire | Name: Cowpea mosaic virus |
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Components |
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-Supramolecule #1: Cowpea mosaic virus
Supramolecule | Name: Cowpea mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12264 / Sci species name: Cowpea mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Vigna unguiculata (cowpea) |
-Macromolecule #1: Cowpea mosaic virus small subunit
Macromolecule | Name: Cowpea mosaic virus small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Cowpea mosaic virus / Strain: SB |
Molecular weight | Theoretical: 20.961564 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: GPVCAEASDV YSPCMIASTP PAPFSDVTAV TFDLINGKIT PVGDDNWNTH IYNPPIMNVL RTAAWKSGTI HVQLNVRGAG VKRADWDGQ VFVYLRQSMN PESYDARTFV ISQPGSAMLN FSFDIIGPNS GFEFAESPWA NQTTWYLECV ATNPRQIQQF E VNMRFDPN FRVAGNILMP PFPLSTETPP L UniProtKB: RNA2 polyprotein |
-Macromolecule #2: Cowpea mosaic virus large subunit
Macromolecule | Name: Cowpea mosaic virus large subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Cowpea mosaic virus / Strain: SB |
Molecular weight | Theoretical: 40.858434 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: MEQNLFALSL DDTSSVRGSL LDTKFAQTRV LLSKAMAGGD VLLDEYLYDV VNGQDFRATV AFLRTHVITG KIKVTATTNI SDNSGCCLM LAINSGVRGK YSTDVYTICS QDSMTWNPGC KKNFSFTFNP NPCGDSWSAE MISRSRVRMT VICVSGWTLS P TTDVIAKL ...String: MEQNLFALSL DDTSSVRGSL LDTKFAQTRV LLSKAMAGGD VLLDEYLYDV VNGQDFRATV AFLRTHVITG KIKVTATTNI SDNSGCCLM LAINSGVRGK YSTDVYTICS QDSMTWNPGC KKNFSFTFNP NPCGDSWSAE MISRSRVRMT VICVSGWTLS P TTDVIAKL DWSIVNEKCE PTIYHLADCQ NWLPLNRWMG KLTFPQGVTS EVRRMPLSIG GGAGATQAFL ANMPNSWISM WR YFRGELH FEVTKMSSPY IKATVTFLIA FGNLSDAFGF YESFPHRIVQ FAEVEEKCTL VFSQQEFVTA WSTQVNPRTT LEA DGCPYL YAIIHDSTTG TISGDFNLGV KLVGIKDFCG IGSNPGIDGS RLL UniProtKB: RNA2 polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.9 mg/mL |
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Buffer | pH: 7.8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / 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 II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 1759 / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 10.0 µm / Nominal defocus min: 0.35000000000000003 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-5msh: |