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- EMDB-19974: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 c... -

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Basic information

Entry
Database: EMDB / ID: EMD-19974
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 central spike protein - knob and petal domains
Map dataPhage phi812 central spike protein - knob and petal domains; postprocessed map
Sample
  • Complex: Central spike protein - knob and petal domains
    • Protein or peptide: GP-PDE domain-containing protein
Keywordsbacteriophage / phage / contractile / phi812 / spike / central spike / TIM / VIRAL PROTEIN
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / GP-PDE domain-containing protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsBinovsky J / Pichel-Beleiro A / van Raaij MJ / 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 / Pichel-Beleiro A / van Raaij MJ / Plevka P
History
DepositionMar 27, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19974.png

Downloads & links

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Map

FileDownload / File: emd_19974.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhage phi812 central spike protein - knob and petal domains; postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.027909704 - 0.06598589
Average (Standard dev.)0.000112777365 (±0.0013928787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19974_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage phi812 central spike protein - knob and...

Fileemd_19974_half_map_1.map
AnnotationPhage phi812 central spike protein - knob and petal domains; half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Phage phi812 central spike protein - knob and...

Fileemd_19974_half_map_2.map
AnnotationPhage phi812 central spike protein - knob and petal domains; half1 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 : Central spike protein - knob and petal domains

EntireName: Central spike protein - knob and petal domains
Components
  • Complex: Central spike protein - knob and petal domains
    • Protein or peptide: GP-PDE domain-containing protein

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Supramolecule #1: Central spike protein - knob and petal domains

SupramoleculeName: Central spike protein - knob and petal domains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus phage 812 (virus)

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Macromolecule #1: GP-PDE domain-containing protein

MacromoleculeName: GP-PDE domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 94.274195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSDDLNVKGL VLATVSKINY KYQSVEVKVN NLTLGSRIGD DGSLAVPYPK SFIGRTPEGS VFGTKPLITE GSVVLIGFLN DDINSPIIL SVYGDNEQNK MINTNPLDGG KFDTESVYKY SSSLYEILPS LNYKYDDGEG TSIRTYNGKS FFSMTSGEEE K PQATDFYT ...String:
GSDDLNVKGL VLATVSKINY KYQSVEVKVN NLTLGSRIGD DGSLAVPYPK SFIGRTPEGS VFGTKPLITE GSVVLIGFLN DDINSPIIL SVYGDNEQNK MINTNPLDGG KFDTESVYKY SSSLYEILPS LNYKYDDGEG TSIRTYNGKS FFSMTSGEEE K PQATDFYT GTEYQDLFTS YYGNKTLIEP RIQKAPNMLF KHQGVFYDDG TPDNHITTLF ISERGDIRAS VLNTETQKRT TQ EMSSDGS YRVIKQDDDL MLDEAQVWIE YGISEDNKFY IKNDKHKFEF TDEGIYIDDK PMLENLDESI AEAMKNLNEI QKE LDDINY LLKGVGKDNL EELIESTKES IEASKKATSD VNRLTTQIAE VSGRTEGIIT QFQKFRDETF KDFYEDASTV INEV NQNFP TMKTDVKTLK TKVDNLEKTE IPNIKTRLTE LENNNNNADK IISDRGEHIG AMIQLEENVT VPMRKYMPIP WSKVT YNNA EFWDSNNPTR LVVPKGITKV RVAGNVLWDS NATGQRMLRI LKNGTYSIGL PYTRDVAIST APQNGTSGVI PVKEGD YFE FEAFQDSEGD RQFRADPYTW FSIEAIELET ETMEKDFMLI GHRGATGYTD EHTIKGYQMA LDKGADYIEL DLQLTKD NK LLCMHDSTID RTTTGTGKVG DMTLSYIQTN FTSLNGEPIP SLDDVLNHFG TKVKYYIETK RPFDANMDRE LLTQLKAK G LIGIGSERFQ VIIQSFARES LINIHNQFSN IPLAYLTSTF SESEMDDCLS YGFYAIAPKY TTITKELVDL AHSKGLKVH AWTVNTKEEM QSLIQMGVDG FFTNYLDEYK KI

UniProtKB: GP-PDE domain-containing 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

Concentration0.8 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMKNaO4P-Sodium Potassium Phosphate
200.0 mMNaClSodium Chloride

Details: sample diluted 10x with water before vitrification
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailssample diluted 10x with water before vitrification

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Electron microscopy

MicroscopeFEI TITAN 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 grids imaged: 1 / Number real images: 3120 / Average exposure time: 8.0 sec. / Average electron dose: 57.0 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: 0.3 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 487160
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated by stochastic gradient descent in Relion
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0beta) / Number images used: 135736
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: 3D Autorefine
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0beta) / Details: 3D Autorefine
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: Other, initial_model_type: experimental modelXray structure
source_name: Other, initial_model_type: in silico modelmanual building
DetailsChimera; Isolde
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9eul:
Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 central spike protein - knob and petal domains

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