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- EMDB-15189: Capsid structure of the L-A helper virus from native viral communities -

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Basic information

Entry
Database: EMDB / ID: EMD-15189
TitleCapsid structure of the L-A helper virus from native viral communities
Map dataIcosahedral symmetrized map for the viral capsid of the Saccharomyces cerevisiae L-A helper virus
Sample
  • Virus: Saccharomyces cerevisiae virus L-A
    • Protein or peptide: Major capsid protein
KeywordsCapsid structure ScVLA / viral particle / wildtype / endogenous / VIRUS
Function / homologyMajor coat protein, L-A virus / L-A virus major coat protein superfamily / L-A virus, major coat protein / viral capsid / Major capsid protein
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae virus L-A
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsSchmidt L / Tueting C / Kyrilis F / Hamdi F / Semchonok DA / Kastritis PL
Funding support Germany, European Union, 5 items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research03Z22HN23 Germany
German Federal Ministry for Education and Research03Z22HI2 Germany
German Federal Ministry for Education and Research03COV04 Germany
German Research Foundation (DFG)391498659 Germany
European Regional Development FundEFRE: ZS/2016/04/78115European Union
CitationJournal: Biorxiv / Year: 2022
Title: Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts
Authors: Schmidt L / Tuting C / Kyrilis FL / Hamdi F / Semchonok DA / Hause G / Meister A / Ihling C / Shah PNM / Stubbs MT / Sinz A / Stuart DI / Kastritis PL
History
DepositionJun 16, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15189.png

Downloads & links

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Map

FileDownload / File: emd_15189.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral symmetrized map for the viral capsid of the Saccharomyces cerevisiae L-A helper virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.57 Å/pix.
x 384 pix.
= 602.035 Å		1.57 Å/pix.
x 384 pix.
= 602.035 Å		1.57 Å/pix.
x 384 pix.
= 602.035 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5678 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-1.0439649 - 3.451766
Average (Standard dev.)0.013144757 (±0.27169263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 602.0352 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Icosahedral symmetrized map for the viral capsid of...

Fileemd_15189_half_map_1.map
AnnotationIcosahedral symmetrized map for the viral capsid of the Saccharomyces cerevisiae L-A helper virus - Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Icosahedral symmetrized map for the viral capsid of...

Fileemd_15189_half_map_2.map
AnnotationIcosahedral symmetrized map for the viral capsid of the Saccharomyces cerevisiae L-A helper virus - Half Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae virus L-A

EntireName: Saccharomyces cerevisiae virus L-A
Components
  • Virus: Saccharomyces cerevisiae virus L-A
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Saccharomyces cerevisiae virus L-A

SupramoleculeName: Saccharomyces cerevisiae virus L-A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11008 / Sci species name: Saccharomyces cerevisiae virus L-A / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 76.070031 KDa
SequenceString: MLRFVTKNSQ DKSSDLFSIC SDRGTFVAHN RVRTDFKFDN LVFNRVYGVS QKFTLVGNPT VCFNEGSSYL EGIAKKYLTL DGGLAIDNV LNELRSTCGI PGNAVASHAY NITSWRWYDN HVALLMNMLR AYHLQVLTEQ GQYSAGDIPM YHDGHVKIKL P VTIDDTAG ...String:
MLRFVTKNSQ DKSSDLFSIC SDRGTFVAHN RVRTDFKFDN LVFNRVYGVS QKFTLVGNPT VCFNEGSSYL EGIAKKYLTL DGGLAIDNV LNELRSTCGI PGNAVASHAY NITSWRWYDN HVALLMNMLR AYHLQVLTEQ GQYSAGDIPM YHDGHVKIKL P VTIDDTAG PTQFAWPSDR STDSYPDWAQ FSESFPSIDV PYLDVRPLTV TEVNFVLMMM SKWHRRTNLA IDYEAPQLAD KF AYRHALT VQDADEWIEG DRTDDQFRPP SSKVMLSALR KYVNHNRLYN QFYTAAQLLA QIMMKPVPNC AEGYAWLMHD ALV NIPKFG SIRGRYPFLL SGDAALIQAT ALEDWSAIMA KPELVFTYAM QVSVALNTGL YLRRVKKTGF GTTIDDSYED GAFL QPETF VQAALACCTG QDAPLNGMSD VYVTYPDLLE FDAVTQVPIT VIEPAGYNIV DDHLVVVGVP VACSPYMIFP VAAFD TANP YCGNFVIKAA NKYLRKGAVY DKLEAWKLAW ALRVAGYDTH FKVYGDTHGL TKFYADNGDT WTHIPEFVTD GDVMEV FVT AIERRARHFV ELPRLNSPAF FRSVEVSTTI YDTHVQAGAH AVYHASRINL DYVKPVSTGI QVINAGELKN YWGSVRR TQ QGLGVVGLTM PAVMPTGEPT AGAAHEELIE QADNVLVE

UniProtKB: Major 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

Concentration0.3 mg/mL
BufferpH: 7.4 / Component - Concentration: 200.0 mM / Component - Formula: CH3COONH4 / Component - Name: Ammoniumacetate
Details: pH of the buffer was adjusted with NaOH buffer was filtered and sonicated
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 2 and blot time 6 s before plunging.
Detailsheterogenous cell extract

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 89297 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 118.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 7020 / Average exposure time: 3.61 sec. / Average electron dose: 30.0 e/Å2

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Image processing

Particle selectionNumber selected: 2725140
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1m1c

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3) / Number images used: 1020420
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1m1c


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe initial model was rigid-fitted by ChimeraX and refined by iterative cycles of Coot and PHENIX.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8a5t:
Capsid structure of the L-A helper virus from native viral communities

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