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- EMDB-28604: Acheta domesticus segmented densovirus high buoyancy fraction 2 e... -

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Basic information

Entry
Database: EMDB / ID: EMD-28604
TitleAcheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure
Map dataAcheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure
Sample
  • Virus: unclassified Densovirinae (virus)
    • Protein or peptide: Capsid protein
Keywordsparvovirus / densovirus / virus capsid / virion / insect virus / capsid / invertebrate / virus / VIRUS LIKE PARTICLE
Function / homologyDensovirus VP1 protein / Capsid protein
Function and homology information
Biological speciesSolenopsis invicta-associated densovirus / unclassified Densovirinae (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPenzes JJ / McKenna R / Tijssen P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
National Institutes of Health/Office of the DirectorOD018142 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR025080 United States
CitationJournal: To Be Published
Title: Structural and molecular biology of Acheta domesticus segmented densovirus, the first parvovirus to harbor a bipartite genome
Authors: Penzes JJ / Pham HT / Chipman P / Smith E / McKenna R / Tijssen P
History
DepositionOct 18, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28604.png

Downloads & links

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Map

FileDownload / File: emd_28604.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.06 Å/pix.
x 500 pix.
= 529. Å		1.06 Å/pix.
x 500 pix.
= 529. Å		1.06 Å/pix.
x 500 pix.
= 529. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-15.600300000000001 - 28.4237
Average (Standard dev.)-0.000000000111263 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 529.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : unclassified Densovirinae

EntireName: unclassified Densovirinae (virus)
Components
  • Virus: unclassified Densovirinae (virus)
    • Protein or peptide: Capsid protein

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Supramolecule #1: unclassified Densovirinae

SupramoleculeName: unclassified Densovirinae / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 185880 / Sci species name: unclassified Densovirinae / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Virus shellShell ID: 1 / Diameter: 210.0 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Solenopsis invicta-associated densovirus
Molecular weightTheoretical: 36.291906 KDa
Recombinant expressionOrganism: Acheta domesticus (house cricket)
SequenceString: EGYGKHITSM HVRNIFNQGN QVIRNIVKQQ RYELLDFTGT EAGTTNLPKI IPYQCIWWRG LQNAANVNQT INNMIALNTI SYGVRFLKA KLCIEVYAVT RKRLIQTGAT SYYTDDFEQG QNLFIGWADR KAESIPITTP ADLDETKLTV ANTTLFDANN D NITKEEVP ...String:
EGYGKHITSM HVRNIFNQGN QVIRNIVKQQ RYELLDFTGT EAGTTNLPKI IPYQCIWWRG LQNAANVNQT INNMIALNTI SYGVRFLKA KLCIEVYAVT RKRLIQTGAT SYYTDDFEQG QNLFIGWADR KAESIPITTP ADLDETKLTV ANTTLFDANN D NITKEEVP TREKWCHTWD LDVLNHNYLW EPNNLDSQWT LIPGAQAVQP TATPIGPTYQ EIVIATKAIG ANESALVTTI QD RRSYPRL MLSQPQIKDE TDTMKFKYQI RISTELEMEH HIKPDIANPW LTRQTLPLPA LSGDGTTRYV PCVPYETHVS Q

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: 7.4 / Component - Concentration: 1.0 x / Component - Name: Phosphate-buffered saline
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV
DetailsDeceased common house crickets, previously showing signs of paralysis, inability to jump, and inability to control movement

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 4.32 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 58680
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio random model based on 100 boxed particles
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48354
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 30

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