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- EMDB-15855: Rosellinia necatrix megabirnavirus 1-W779 full capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-15855
TitleRosellinia necatrix megabirnavirus 1-W779 full capsid
Map data
Sample
  • Virus: Rosellinia necatrix megabirnavirus 1/W779
    • Protein or peptide: Major capsid protein A
Keywordsviruses / dsRNA / capsid / cryo-EM / fungus / Megabirnaviridae / mycoviruses / VIRUS
Function / homologyCoat protein
Function and homology information
Biological speciesRosellinia necatrix megabirnavirus 1/W779
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang H / Okamoto K / Miyazaki N / Suzuki N
Funding support Sweden, Japan, 2 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: 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
DepositionSep 21, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15855.png

Downloads & links

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Map

FileDownload / File: emd_15855.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 580 pix.
= 649.6 Å		1.12 Å/pix.
x 580 pix.
= 649.6 Å		1.12 Å/pix.
x 580 pix.
= 649.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.23526236 - 0.41076756
Average (Standard dev.)0.0016008583 (±0.024353076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-290-290-290
Dimensions580580580
Spacing580580580
CellA=B=C: 649.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15855_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15855_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Rosellinia necatrix megabirnavirus 1/W779

EntireName: Rosellinia necatrix megabirnavirus 1/W779
Components
  • Virus: Rosellinia necatrix megabirnavirus 1/W779
    • Protein or peptide: Major capsid protein A

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Supramolecule #1: Rosellinia necatrix megabirnavirus 1/W779

SupramoleculeName: 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: Major capsid protein A

MacromoleculeName: Major capsid protein A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rosellinia necatrix megabirnavirus 1/W779 / Strain: isolate -/Japan/W779/2001
Molecular weightTheoretical: 136.084953 KDa
SequenceString: MSGDNGVYSG SAAYNTATAP KVPVSRATFF QNTKSKDFDF KFADGADAIA NVLQQMEHGV AQHQLGDMNV RTDGLATVSA VLNGRKRKI ANQYMMHFDL FGRAARSTVR MESRIQSFGE GKDVDNFMAK FHNQLSGVYE RRSEGVANFG RILATDTDLG G TSGLSVVF ...String:
MSGDNGVYSG SAAYNTATAP KVPVSRATFF QNTKSKDFDF KFADGADAIA NVLQQMEHGV AQHQLGDMNV RTDGLATVSA VLNGRKRKI ANQYMMHFDL FGRAARSTVR MESRIQSFGE GKDVDNFMAK FHNQLSGVYE RRSEGVANFG RILATDTDLG G TSGLSVVF NGLLRGLHHV STVPTPNVAN LPIRNNRDGA GAVVGRGDMP GREFMDSSRI LPPRSSRWYG APGQPIVPPA PN NPPAHVA PMETVMAGLQ KTVMNELNRV IVSIADVPKL PAHRIRNLIA VLAAVSKPNL GFDANRLEDH SCFTKGWLGF NDI LLFPLT VDLFDRVVAN EAGVNDAGFI VPNAAPPQFL QNTNQQVIDF RGVGVGQAGD IPALRLAQSW SDAIGFLLDT IGGE AQLAM GLNDMVAQCF HMHGAQTTML STPIISRADF GVYHNVVTNM YRRLAYMYTR LIRTNAAAGG GAMLDRQHYQ WPTHA KVGF HDDTAVNAAA AAARIHDGLR QPLLDEAFGA GVVQPGNMDL VGAGIDFTRD LTSSLGKAYP EHRPIGADDN KRDLGD FTA GTVDAAASGY EWDNYVYRLF GNMSAMRSKA EFDRLLATFP SSTLSELFIW MGNVGFADTW EERWGYDAAP LCSIPIP AG HDRSMLRNWS WVNVHNVHSV TGTSENVVLA GYVGLSRTHD YIMDTRSTPA TSQGRRLAAM FYYTNADKML SLTFGLAG Q LRAAADTTVA KFQICPHTIA RAQGYIMTDN DPLSDELKGT DFVTEQFSLA GLTNLYLGYF DGLATRLGIY DLRYTYSEY AECRVELHGI QRNFLTDRLD AFVSYKCLHP IMFEYYMCGA NISGGILNGD KAYEQVEMGN IRAYDAMFDT SAARDFNFVG VRGASQQIA AVGGFHIQYK MEVEIQRPGD GTEASRFNVY ERYLNNYLRM SDCAPTSVLN AVSPLFWMAG TTRVVLCEAA N GYKPMAYD ISQTSFWNRE NGLWAFTWGE SEKTHRPNAI PHGTRRLGNS EVLMNSRFSK ILDKKGITKL ETRVGGRKRG DN NDDFVAA DTRMFIIQDV AGGEHAAYSS LRDPGFALVR AAHTWDTFVQ NPRMLLLERG YGNTGFTDTY SAAGIRRTNG HIS LRLSAL TDDFEFTMHP LARAEYKETS RVSLTSMIYV GTAGKDLSLP TGTVEDIIGA VDGMRRVVRT IGGQTIKTAP VVPP TEQRD MVQEERVGTP VKNAGNANPA ADSDNATEGV VEPKN

UniProtKB: Coat protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12230
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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