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- EMDB-53922: Cryo-EM structure of Yadonushi Virus 1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53922
TitleCryo-EM structure of Yadonushi Virus 1
Map dataSharpened map of YnV1 capsid
Sample
  • Virus: Yadonushi Virus 1
    • Protein or peptide: Coat protein
    • Protein or peptide: Coat protein
KeywordsCryoEM / Virion / Yadokari / Mycovirus / VIRUS
Function / homologyE3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / Zinc finger, CCCH-type superfamily / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / viral capsid / zinc ion binding / Coat protein
Function and homology information
Biological speciesRosellinia necatrix (fungus) / Yadonushi Virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsNovoa G / Suzuki N / Caston JR
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-146143NB-I00 Spain
CitationJournal: To Be Published
Title: Cryo-EM structure of Yadonushi Virus 1 at 2.2 Angstroms resolution
Authors: Novoa G / Suzuki N / Caston JR
History
DepositionMay 29, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53922.png

Downloads & links

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Map

FileDownload / File: emd_53922.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of YnV1 capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 640 pix.
= 684.8 Å		1.07 Å/pix.
x 640 pix.
= 684.8 Å		1.07 Å/pix.
x 640 pix.
= 684.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.82998455 - 1.4632077
Average (Standard dev.)0.002652904 (±0.07718062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 684.80005 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of YnV1 capsid

Fileemd_53922_additional_1.map
AnnotationUnsharpened map of YnV1 capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of YnV1 capsid

Fileemd_53922_half_map_1.map
AnnotationHalf map A of YnV1 capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of YnV1 capsid

Fileemd_53922_half_map_2.map
AnnotationHalf map B of YnV1 capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yadonushi Virus 1

EntireName: Yadonushi Virus 1
Components
  • Virus: Yadonushi Virus 1
    • Protein or peptide: Coat protein
    • Protein or peptide: Coat protein

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Supramolecule #1: Yadonushi Virus 1

SupramoleculeName: Yadonushi Virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: R. necatrix strain W1032 contains different type of Yadonushi Virus 1: strain A, B and C.
NCBI-ID: 2094187 / Sci species name: Yadonushi Virus 1 / Sci species strain: A, B, C / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Rosellinia necatrix (fungus) / Strain: W1032
Virus shellShell ID: 1 / Diameter: 540.0 Å / T number (triangulation number): 1

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rosellinia necatrix (fungus)
Molecular weightTheoretical: 111.298672 KDa
SequenceString: TTFSNFMTNV LGKTSSSKGV ISLKQISSSI SHLIPDTPRA DTNNNRASYF YRVRRLLTRA MRNQSVPYVP VYEHNPVASY KIVRYDTFE VSNKLVLKKA KTVDVSARSI SLTQDISLST LKAEIIDSTN NIKTFNNNWI TMMDVQKPIA DVFKVLSLRS E NNRVFWDT ...String:
TTFSNFMTNV LGKTSSSKGV ISLKQISSSI SHLIPDTPRA DTNNNRASYF YRVRRLLTRA MRNQSVPYVP VYEHNPVASY KIVRYDTFE VSNKLVLKKA KTVDVSARSI SLTQDISLST LKAEIIDSTN NIKTFNNNWI TMMDVQKPIA DVFKVLSLRS E NNRVFWDT GLYNYFSNFA DVTSSSFFPI ALNKTLRHHA MTSSMSIGAF NQLEARTPDL KFDPLVAEPK IQDKLYPLFN HD ISDINAY TVPLPVFIFM MFPQHFRKEI IVDYMLAFSF GNRTINEREN FLLQAIRPRL QEILTLNAEP VQLPTNAHDF AIK LDNIGV FIEGLTTSAP AVRSFFDSLH KLSTGYADFR IRGTPLRAIN LPFTVILSED FDQTTRATVP LNENDFLKKH DAIE KMVSM LPHPIFQYAI EVEQTINLPG NGQNTLAKNT SKDLFMPVAS LVNQFHKKNQ LLCVDIVPHQ GGSIRSNFTY NDGTV ASEY RYPITLLSKD GTKAKVDIID QMTKPVSVLK DIKEHLTYSR DNVNRLNASM NQSMSCMLTE TELADLLNLT ANLTHV TPL PTTVHDISQT EDKLDIHYIN TPRIGLTGYK IKADDMTDDE YIISDTYVAN VTDGITNVAF NRFRDHTPSS DLGGANK FI AHPDYVIPFF DHDWFVFITA GLLNFQWPDI IGKVTTNTVF EHNATLDAIA TEQIRLIDTY TDTKNIPMRD TFFPPGND V RDSLEVISIT NSIAMDDSVL NQVAHAFSTQ SYTCSHPYKL DYDGNEYLDN LLACSTNHVP IRFTQMNMVN PLPILSNLE KDFERATINN TPNKEGVVRS QRRRRPEDNF LRMITQIITR FDFSGFSTVN ENNMVTLRDA ATNQKISAYQ RYTTNLSQIK YFISLCIRL GTLQTFNDIT GTSTTRVKTP TYPTHLLAVN VITQTEYRIS LNKEEYWSHL KSSIVITTPT DVSVEQEQIF D DININRNV NRVKPSFSNL

UniProtKB: Coat protein

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Macromolecule #2: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rosellinia necatrix (fungus)
Molecular weightTheoretical: 115.597586 KDa
SequenceString: IKKMFDTQTN LYNAIRNTAM TMNIPLTSQL DTATLPPAST TFSNFMTNVL GKTSSSKGVI SLKQISSSIS HLIPDTPRAD TNNNRASYF YRVRRLLTRA MRNQSVPYVP VYEHNPVASY KIVRYDTFEV SNKLVLKKAK TVDVSARSIS LTQDISLSTL K AEIIDSTN ...String:
IKKMFDTQTN LYNAIRNTAM TMNIPLTSQL DTATLPPAST TFSNFMTNVL GKTSSSKGVI SLKQISSSIS HLIPDTPRAD TNNNRASYF YRVRRLLTRA MRNQSVPYVP VYEHNPVASY KIVRYDTFEV SNKLVLKKAK TVDVSARSIS LTQDISLSTL K AEIIDSTN NIKTFNNNWI TMMDVQKPIA DVFKVLSLRS ENNRVFWDTG LYNYFSNFAD VTSSSFFPIA LNKTLRHHAM TS SMSIGAF NQLEDRTPDL KFDPLVAEPK IQDKLYPLFN HDISDINAYT VPLPVFIFMM FPQHFRKEII VDYMLAFSFG NRT INEREN FLLQAIRPRL QEILTLNAEP VQLPTNAHDF AIKLDNIGAF IEGLTTSAPA VRSFFDSLHK LSTGYADFRI RGTP LRAIN LPFTVILSED FDQTTRATVP LNENDFLKKH DAIEKMVSML PHPIFQYAIE VEQTINLPGN GQNTLAKNTS KDLFM PVAS LVNQFHKKNQ LLCVDIVPHQ GGSIRSNFTY NDGTVASEYR YPITLLSKDG TKAKVDIIDQ MTKPVSVLKD IKEHLT YSR DNVNRLNASM NQSMSCMLTE TELADLLNLT ANLTHVTPLP TTVHDISQTE DKLDIHYINT PRIGLTGYKI KADDMTD DE YIISDTYVAN VTDGITNVAF NRFRDHTPSS DLGGANKFIA HPDYVIPFFD HDWFVFITAG LLNFQWPDII GKATTNTV F EHNATLDAIA TQQIRLIDTY TDTKNIPMRD TFFPPGNDVR DSLEVISITN SIAMDDSVLN QVAHAFSTQS YTCSHPYKL DYDGNEYLDN LLACSTNHVP IRFTQMNMVN PLPILSNLEK DFERATINNT PNKEGVVRSQ RRRRPEDNFL RMITQIITRF DFSGFSTVN ENNMVTLRDA ATNQKISAYQ RYTTNLSQIK YFISLCIRLG TLQTFNDITG TSTTRVKTPT YPTHLLAVNV I TQTEYRIS LNKEEYWSHL KSSIVITTPT DVSVEQEQIF DDININRNVN RVKPSFSNL

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 / Details: Phosphate buffer 0.05M
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 550000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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