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- EMDB-50094: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 t... -

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Basic information

Entry
Database: EMDB / ID: EMD-50094
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 tail in the post-contraction state - sheath proteins
Map dataPhage phi812 tail in the post-contraction state - sheath; postprocessed map
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Complex: Tail
      • Complex: Tail sheath
        • Protein or peptide: Major tail sheath protein
Keywordsbacteriophage / phage / contractile / phi812 / tail / VIRUS
Function / homologyMajor tail sheath protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBinovsky J / Siborova M / Skubnik K / Novacek J / Plevka P
Funding supportEuropean Union, Czech Republic, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: To Be Published
Title: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky J / Siborova M / Skubnik K / Novacek J / Plevka P
History
DepositionApr 15, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50094.png

Downloads & links

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Map

FileDownload / File: emd_50094.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage phi812 tail in the post-contraction state - sheath; postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 430. Å		1.08 Å/pix.
x 400 pix.
= 430. Å		1.08 Å/pix.
x 400 pix.
= 430. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.075 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.3792962 - 0.46727976
Average (Standard dev.)0.00017030507 (±0.026963748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50094_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage phi812 tail in the post-contraction state - sheath; half1 map

Fileemd_50094_half_map_1.map
AnnotationPhage phi812 tail in the post-contraction state - sheath; half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage phi812 tail in the post-contraction state - sheath; half2 map

Fileemd_50094_half_map_2.map
AnnotationPhage phi812 tail in the post-contraction state - sheath; half2 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 : Staphylococcus phage 812

EntireName: Staphylococcus phage 812 (virus)
Components
  • Virus: Staphylococcus phage 812 (virus)
    • Complex: Tail
      • Complex: Tail sheath
        • Protein or peptide: Major tail sheath protein

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Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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Supramolecule #2: Tail

SupramoleculeName: Tail / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Staphylococcus phage 812 (virus)

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Supramolecule #3: Tail sheath

SupramoleculeName: Tail sheath / type: complex / ID: 3 / Parent: 2 / Macromolecule list: all
Source (natural)Organism: Staphylococcus phage 812 (virus)

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Macromolecule #1: Major tail sheath protein

MacromoleculeName: Major tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 64.559008 KDa
SequenceString: MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILA MRIEDAKPAS AEIGGLKITS KIYGNVANNI QVGLEKNTLS DSLRLRVIFQ DDRFNEVYDN IGNIFTIKYK G EEANATFS ...String:
MAVEPFPRRP ITRPHASIEV DTSGIGGSAG SSEKVFCLIG QAEGGEPNTV YELRNYSQAK RLFRSGELLD AIELAWGSNP NYTAGRILA MRIEDAKPAS AEIGGLKITS KIYGNVANNI QVGLEKNTLS DSLRLRVIFQ DDRFNEVYDN IGNIFTIKYK G EEANATFS VEHDEETQKA SRLVLKVGDQ EVKSYDLTGG AYDYTNAIIT DINQLPDFEA KLSPFGDKNL ESSKLDKIEN AN IKDKAVY VKAVFGDLEK QTAYNGIVSF EQLNAEGEVP SNVEVEAGEE SATVTATSPI KTIEPFELTK LKGGTNGEPP ATW ADKLDK FAHEGGYYIV PLSSKQSVHA EVASFVKERS DAGEPMRAIV GGGFNESKEQ LFGRQASLSN PRVSLVANSG TFVM DDGRK NHVPAYMVAV ALGGLASGLE IGESITFKPL RVSSLDQIYE SIDLDELNEN GIISIEFVRN RTNTFFRIVD DVTTF NDKS DPVKAEMAVG EANDFLVSEL KVQLEDQFIG TRTINTSASI IKDFIQSYLG RKKRDNEIQD FPAEDVQVIV EGNEAR ISM TVYPIRSFKK ISVSLVYKQQ TLQA

UniProtKB: Major tail sheath 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: 8 / Details: 50mM Tris, 10mM NaCl, 10mM CaCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / 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

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number real images: 15371 / Average exposure time: 7.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 106091
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

4052

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 69969
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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