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Yorodumi- EMDB-15859: Rosellinia necatrix megabirnavirus 1-W779 full capsid with Crown ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15859 | |||||||||
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Title | Rosellinia necatrix megabirnavirus 1-W779 full capsid with Crown protein | |||||||||
Map data | ||||||||||
Sample |
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Keywords | viruses / dsRNA / capsid / cryo-EM / fungus / Megabirnaviridae / mycoviruses / VIRUS | |||||||||
Function / homology | membrane / MchC protein Function and homology information | |||||||||
Biological species | Rosellinia necatrix megabirnavirus 1/W779 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Wang H / Okamoto K / Miyazaki N / Suzuki N | |||||||||
Funding support | Sweden, Japan, 2 items
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Citation | Journal: PLoS Pathog / Year: 2023 Title: Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture. Authors: Han Wang / Lakha Salaipeth / Naoyuki Miyazaki / Nobuhiro Suzuki / Kenta Okamoto / Abstract: Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces ...Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces a lethal plant disease white root rot. Herein, we have first resolved the atomic structure of the RnMBV1 capsid at 3.2 Å resolution using cryo-electron microscopy (cryo-EM) single-particle analysis. Compared with other non-enveloped icosahedral dsRNA viruses, the RnMBV1 capsid protein structure exhibits an extra-long C-terminal arm and a surface protrusion domain. In addition, the previously unrecognized crown proteins are identified in a symmetry-expanded cryo-EM model and are present over the 3-fold axes. These exclusive structural features of the RnMBV1 capsid could have been acquired for playing essential roles in transmission and/or particle assembly of the megabirnaviruses. Our findings, therefore, will reinforce the understanding of how the structural and molecular machineries of the megabirnaviruses influence the virulence of the disease-related ascomycete fungus. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15859.map.gz | 689.1 MB | EMDB map data format | |
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Header (meta data) | emd-15859-v30.xml emd-15859.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_15859.png | 236.3 KB | ||
Filedesc metadata | emd-15859.cif.gz | 5.9 KB | ||
Others | emd_15859_half_map_1.map.gz emd_15859_half_map_2.map.gz | 598.9 MB 599.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15859 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15859 | HTTPS FTP |
-Validation report
Summary document | emd_15859_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_15859_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_15859_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | emd_15859_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15859 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15859 | HTTPS FTP |
-Related structure data
Related structure data | 8b59MC 8b4zC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15859.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15859_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15859_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rosellinia necatrix megabirnavirus 1/W779
Entire | Name: Rosellinia necatrix megabirnavirus 1/W779 |
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Components |
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-Supramolecule #1: Rosellinia necatrix megabirnavirus 1/W779
Supramolecule | Name: Rosellinia necatrix megabirnavirus 1/W779 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 658904 / Sci species name: Rosellinia necatrix megabirnavirus 1/W779 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: RnMBV1 Crown protein
Macromolecule | Name: RnMBV1 Crown protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Rosellinia necatrix megabirnavirus 1/W779 / Strain: isolate -/Japan/W779/2001 |
Molecular weight | Theoretical: 151.8835 KDa |
Sequence | String: MGITYRDAQI FSACVEALSA RNNRITLTSF PLTAGQGQAP TATPAWYPVD LFVADATAVY GRRQLFAWTV DKVRPTRNVA FVTDRVAMD FSAALLSLMA ELEAVAPDVY AAIHGGATPG ADLGDRITQL ENRRVGCLAY VMATVVRAPI THNVRSFSAM L ASDPQAHA ...String: MGITYRDAQI FSACVEALSA RNNRITLTSF PLTAGQGQAP TATPAWYPVD LFVADATAVY GRRQLFAWTV DKVRPTRNVA FVTDRVAMD FSAALLSLMA ELEAVAPDVY AAIHGGATPG ADLGDRITQL ENRRVGCLAY VMATVVRAPI THNVRSFSAM L ASDPQAHA ALLAYLTPNS AGQLDGAPIY FRRSDVDLRN NHLALHAEVV PGLPNMVPLT KAMVEVALAN VEWWSDPLGY DS LTSFGGL ELLSLCDALA VCELSVAYGL KESGYCYLRF AGGCPLAEVI LARLGYNPPL GVAVGWALYN GIKLDWYSKV ISV GHNMRL HVCDTAGEAN ACLIDVLTGE YDGMPVGGVD TVSCWVEQLD LLAAAAGVGR NLSNLHCGVQ TPPRTINTTR RRLL ASLVR TLIADPTLTD EELLHGAVRG TLNGLPRDRA LWRCLQVVNT TVREFLAQDL DAMVRDRREC TTYASRAAFA ERCAM SGNA SGLVGRQYSD MPAALEGEAR ACGLSAIDAI EIVRVVASGE PIRVLLDQHG RPATRPNGRL TADELRRCRP LVVGQG GQV GFLPFVPFIV GGVGATVAAA SGLALATFAT VTGAGAVALG GLGLGAGVAA LSITVGQLSY QVTRRALTTI LPGGREF GL DDLTRVLGGM VGRYISFVDT WFAHGRGDVF QETDAVPAGT VVFVLPNIEY EVLELRERAL GRWSTLLVTT PNGVIAMR A NGALPLRVVD AREAGQTFEW STAARRRFTR AQANAINMMV TASKRVPGLK GSIDAAPSQG TGGSGTDLAG ILQRLSALE QTSVPRAEFD ALQGRVAACE AKITELEADR VPRIDFTELR DRVHHIDGIG LSCLAHLARD LGITVPHNVR TFRQMRANVG EVIWARFVD AVAESFSPMG GRPIFVRTDP AQPRNNHVSL VDEPTTTGFN GTVTPAMRRL TVADLTGDLV DTEWFSWTPY D ASGPLGGT IEGIEAYLTD FTSKLKAELE ATPTRTELGV AVGTRAPPLS DRLAAVERVI GMQEGNQVWR SNELRELWVA ID SIVTGRG QREFTTATIK WPAAFPSAVA TAGRSFGQPG LAGYGELCTL ARQLNALVAG VRNGVVSGMT RNGAGVLQLS TIS SATGNL TSDQQAVLRA CFFPATPRVG EYQIVYPVGG TMGLTRVDPS TNSSIGQYTR ESLVAARNAM PRFAVHTTTP DTVG VAWDN QSAAGLPMGA APVLTVSVNQ LSGVPVTEAD KQRWDAKQDK FKIVNTDDRV AALSWVDSVD GFAAPGSDML LDYQA PAGT GSLPFGSKYA MAVAIGGSLG SQLSEAQVSA ARVVLGNGVW RDAVIDVLRK LHNVMYGGKY GRIDDIAAMR SYLNDG TGL LPGSEPIVDV GGAEGNACAR ATILLRGFSS TMVGVDLKIQ MLVELYGAEP ATAALLYRGW TMQ UniProtKB: MchC protein |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 244609 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |