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- EMDB-40564: CUS-3 Mature Virus Capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-40564
TitleCUS-3 Mature Virus Capsid
Map dataSingle Particle Reconstruction of CUS3 Bacteriophage
Sample
  • Virus: Enterobacteria phage CUS-3 (virus)
    • Protein or peptide: Putative coat protein
KeywordsBacteriophage / Capsid / Virus
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral capsid / Putative coat protein
Function and homology information
Biological speciesEnterobacteria phage CUS-3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWhitehead III RD / Alexandrescu AT / White S / Teschke CM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM076661 United States
CitationJournal: To Be Published
Title: Not currently available
Authors: Whitehead III RD / White S / Alexandrescu AT / Teschke CM
History
DepositionApr 19, 2023-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40564.png

Downloads & links

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Map

FileDownload / File: emd_40564.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle Particle Reconstruction of CUS3 Bacteriophage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.94 Å/pix.
x 800 pix.
= 748. Å		0.94 Å/pix.
x 800 pix.
= 748. Å		0.94 Å/pix.
x 800 pix.
= 748. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-8.057097000000001 - 15.758607
Average (Standard dev.)0.000000000002079 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 748.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_40564_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_40564_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterobacteria phage CUS-3

EntireName: Enterobacteria phage CUS-3 (virus)
Components
  • Virus: Enterobacteria phage CUS-3 (virus)
    • Protein or peptide: Putative coat protein

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Supramolecule #1: Enterobacteria phage CUS-3

SupramoleculeName: Enterobacteria phage CUS-3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 539221 / Sci species name: Enterobacteria phage CUS-3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 7

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Macromolecule #1: Putative coat protein

MacromoleculeName: Putative coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage CUS-3 (virus)
Molecular weightTheoretical: 44.772359 KDa
SequenceString: ANQLAKDLEI MFENYVEGFE AACVVSRNAK KFRPGDTAMQ RAGDVLYRPQ HYHMNIEEGL DLSSKTPTAL VQRLVPSVFK EPKNILYTL DAREMRDPEH KTEAGRAAGM RLAAQIDSDL ISMVTQRATN VITMADSTAG TQGRDLWNCA AGIDATMTAI G VPQGINRR ...String:
ANQLAKDLEI MFENYVEGFE AACVVSRNAK KFRPGDTAMQ RAGDVLYRPQ HYHMNIEEGL DLSSKTPTAL VQRLVPSVFK EPKNILYTL DAREMRDPEH KTEAGRAAGM RLAAQIDSDL ISMVTQRATN VITMADSTAG TQGRDLWNCA AGIDATMTAI G VPQGINRR SFWNPFNYKD LAGELGHRAY AQGATLTAYE KAQIPPVASF DSYKTDISGR LPKGSTESLT VSGQPEHKVE AK DSNGMPV DNRQGTITVS ASGLQVGDAF TIAGVNSVHQ ITKDTTGQPQ VFRVLAVSGT TVTISPKILP VENTDVASRP YAN VDAKPA ESAAITILNK NAAPANLFWA DGSVELMYGK LAFPTGQGPQ VMTATTEQGA TLIMSYAFDH IKGVTTARFT TLYG CSVLV PEYTGIVIAG Q

UniProtKB: Putative 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: 7.4
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.3075 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34727
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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