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Yorodumi- EMDB-4610: CryoEM reconstructuion of Cowpea Mosaic Virus (CPMV) bound to an ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4610 | ||||||||||||
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Title | CryoEM reconstructuion of Cowpea Mosaic Virus (CPMV) bound to an Affimer reagent | ||||||||||||
Map data | postprocessed map of cryoEM map of Cowpea Mosaic virus bound to an Affimer protein | ||||||||||||
Sample |
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Keywords | VIRUS / CPMV / COMOVIRIDAE / PICORNAVIRALES / AFFIMEr REAGENT / antibody-like | ||||||||||||
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 / : / host cell nucleus / GTP binding / structural molecule activity / DNA binding / RNA binding Similarity search - Function | ||||||||||||
Biological species | synthetic construct (others) / Cowpea mosaic virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Hesketh EL / Tiede C | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2015 Title: Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM. Authors: Emma L Hesketh / Yulia Meshcheriakova / Kyle C Dent / Pooja Saxena / Rebecca F Thompson / Joseph J Cockburn / George P Lomonossoff / Neil A Ranson / Abstract: Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of ...Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly. | ||||||||||||
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_4610.map.gz | 30.1 MB | EMDB map data format | |
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Header (meta data) | emd-4610-v30.xml emd-4610.xml | 22.7 KB 22.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4610_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_4610.png | 315 KB | ||
Filedesc metadata | emd-4610.cif.gz | 6.7 KB | ||
Others | emd_4610_half_map_1.map.gz emd_4610_half_map_2.map.gz | 166.3 MB 166.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4610 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4610 | HTTPS FTP |
-Validation report
Summary document | emd_4610_validation.pdf.gz | 189.7 KB | Display | EMDB validaton report |
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Full document | emd_4610_full_validation.pdf.gz | 189.3 KB | Display | |
Data in XML | emd_4610_validation.xml.gz | 500 B | Display | |
Data in CIF | emd_4610_validation.cif.gz | 371 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4610 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4610 | HTTPS FTP |
-Related structure data
Related structure data | 6qozMC 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_4610.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocessed map of cryoEM map of Cowpea Mosaic virus bound to an Affimer protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Unfiltered half map of cryoEM map of Cowpea...
File | emd_4610_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map of cryoEM map of Cowpea Mosaic virus bound to an Affimer protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map of cryoEM map of Cowpea...
File | emd_4610_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map of cryoEM map of Cowpea Mosaic virus bound to an Affimer protein | ||||||||||||
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: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #3: Affimer
Supramolecule | Name: Affimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: synthetic construct (others) |
-Supramolecule #2: Cowpea mosaic virus
Supramolecule | Name: Cowpea mosaic virus / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 / 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: Cowpea mosaic virus |
-Macromolecule #1: RNA2 polyprotein
Macromolecule | Name: RNA2 polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / 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: 4 / 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 |
-Macromolecule #3: Affimer binding protein
Macromolecule | Name: Affimer binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.286674 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ENSLEIEELA RFAVDEHNKK ENALLEFVRV VKAKEQVVAG TMYYLTLEAK DGGKKKLYEA KVWVKPWENF KELQEFKPV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: LEICA EM GP |
-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: 2980 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |