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- EMDB-17662: Cryo-EM structure of Atkinsonella Hypoxylon Virus-like particles. -

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Basic information

Entry
Database: EMDB / ID: EMD-17662
TitleCryo-EM structure of Atkinsonella Hypoxylon Virus-like particles.
Map dataGlobally sharpened map from RELION post process.
Sample
  • Virus: Atkinsonella hypoxylon virus
    • Protein or peptide: Capsid protein
KeywordsPartitivirus / plant virus / virus like particle / VLP.
Function / homologyviral capsid / Capsid protein
Function and homology information
Biological speciesAtkinsonella hypoxylon (fungus) / Atkinsonella hypoxylon virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsByrne MJ / Sainsbury F
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Cryo-EM structure of Atkinsonella Hypoxylon Virus-like particles.
Authors: Byrne MJ / Sainsbury F
History
DepositionJun 19, 2023-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17662.png

Downloads & links

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Map

FileDownload / File: emd_17662.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobally sharpened map from RELION post process.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.448 Å		0.83 Å/pix.
x 512 pix.
= 424.448 Å		0.83 Å/pix.
x 512 pix.
= 424.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.06729223 - 0.10205845
Average (Standard dev.)0.0004346245 (±0.008594679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Locally sharpened map from deepEMhancer.

Fileemd_17662_additional_1.map
AnnotationLocally sharpened map from deepEMhancer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17662_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17662_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Atkinsonella hypoxylon virus

EntireName: Atkinsonella hypoxylon virus
Components
  • Virus: Atkinsonella hypoxylon virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: Atkinsonella hypoxylon virus

SupramoleculeName: Atkinsonella hypoxylon virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Virus-like particle expressed in plants. / NCBI-ID: 37961 / Sci species name: Atkinsonella hypoxylon virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Atkinsonella hypoxylon (fungus)
Virus shellShell ID: 1 / Diameter: 380.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Atkinsonella hypoxylon (fungus)
Molecular weightTheoretical: 73.747297 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MSSNDSAQTR NLQEERFNER TSTPTVVTAV LPDTNGPTTN STSGSVGPPH PTPNVPVPTQ SSSDPPSASG IFAKEIDLPR NVIQHSGNK FILDVVPDSR FPTFAITEFV QRSFSNFTFE QYSYVSPASL VGYLVYMIHA FVFLVDAFER SPMSAYASEI D ASHAYLRI ...String:
MSSNDSAQTR NLQEERFNER TSTPTVVTAV LPDTNGPTTN STSGSVGPPH PTPNVPVPTQ SSSDPPSASG IFAKEIDLPR NVIQHSGNK FILDVVPDSR FPTFAITEFV QRSFSNFTFE QYSYVSPASL VGYLVYMIHA FVFLVDAFER SPMSAYASEI D ASHAYLRI IDAFSDAYIP DFLFEILDTY LSHRLDIRSK LEMNVSYGSV LYKYDAPRIV APSIFLLAHN QLISQSREST AY EKWLDSI VIHYSRAVIR VGNLVGGLYQ SSHGSTTTHF TYRNWFARSL SRLADSATHR THLRRPMISE FDYNIPSVNN NTY NPYVHL LMLEPNNRNI TLDFIRSLSS FCSTELKATR TLRDHISRRS AAISRCVIKG PEAPTWHSSP LDDLKEKSKQ GNFS QFCEV AKFGLPRKEN SESYTFKFPK DASTIDTAFY LIQENGRSSV LDPTTADEEL HTEGMNLLFD PYDDESSAHY ATVLS GKLI QNSNIDGETL LLPDPTTGLA RTNSRYLQGS VLIRNVLPEF DQHEIRLFPR YPQISRLSAS LTLLFNMRQV WIPRFK QKV DEQPKLSNFS WNEGCDGTVP SLNVVTAESS TNGPAAEQQV ILWSSYRHVS NSDRPTVDTV YYYSTLELLF GTRSSMM QT YNLHQLLSLH

UniProtKB: Capsid 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

Concentration1 mg/mL
BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27700
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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