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- EMDB-29027: CryoEM structure of bacteriophage Q-beta coat protein dimer with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-29027
TitleCryoEM structure of bacteriophage Q-beta coat protein dimer with AYGG linker
Map dataFinal map
Sample
  • Virus: Qubevirus durum
    • Protein or peptide: Minor capsid protein A1 fusion
Keywordscoat protein / q-beta / fusion / VIRUS LIKE PARTICLE
Function / homologyRead-through domain / Read-through domain / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / viral capsid / structural molecule activity / Minor capsid protein A1
Function and homology information
Biological speciesQubevirus durum
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsNewton TP / Zhao L / Finn MG / Kopylov M
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: To Be Published
Title: CryoEM structure of bacteriophage Q-beta coat protein dimer with AYGG linker
Authors: Newton TP / Zhao L / Kopylov M / Finn MG
History
DepositionDec 6, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29027.png

Downloads & links

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Map

FileDownload / File: emd_29027.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 437.76 Å		0.86 Å/pix.
x 512 pix.
= 437.76 Å		0.86 Å/pix.
x 512 pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.358
Minimum - Maximum-0.38012695 - 0.934557
Average (Standard dev.)-0.001355592 (±0.05018903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29027_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Final half map A

Fileemd_29027_half_map_1.map
AnnotationFinal half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Final half map B

Fileemd_29027_half_map_2.map
AnnotationFinal 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 : Qubevirus durum

EntireName: Qubevirus durum
Components
  • Virus: Qubevirus durum
    • Protein or peptide: Minor capsid protein A1 fusion

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Supramolecule #1: Qubevirus durum

SupramoleculeName: Qubevirus durum / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 39803 / Sci species name: Qubevirus durum / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Minor capsid protein A1 fusion

MacromoleculeName: Minor capsid protein A1 fusion / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Qubevirus durum
Molecular weightTheoretical: 28.604137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AKLETVTLGN IGKDGKQTLV LNPRGVNPTN GVASLSQAGA VPALEKRVTV SVSQPSRNRK NYKVQVKIQN PTACTANGSC DPSVTRQAY ADVTFSFTQY STDEERAFVR TELAALLASP LLIDAIDQLN PAYAYGGAKL ETVTLGNIGK DGKQTLVLNP R GVNPTNGV ...String:
AKLETVTLGN IGKDGKQTLV LNPRGVNPTN GVASLSQAGA VPALEKRVTV SVSQPSRNRK NYKVQVKIQN PTACTANGSC DPSVTRQAY ADVTFSFTQY STDEERAFVR TELAALLASP LLIDAIDQLN PAYAYGGAKL ETVTLGNIGK DGKQTLVLNP R GVNPTNGV ASLSQAGAVP ALEKRVTVSV SQPSRNRKNY KVQVKIQNPT ACTANGSCDP SVTRQAYADV TFSFTQYSTD EE RAFVRTE LAALLASPLL IDAIDQLNPA Y

UniProtKB: Minor capsid protein A1

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 64.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 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: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1380
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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