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- PDB-9euk: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 b... -

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Basic information

Entry
Database: PDB / ID: 9euk
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 baseplate in the post-contraction state - sheath initiator, wedge module, and inner tripod proteins
Components
  • Baseplate component
  • Baseplate wedge subunit
  • DUF4815 domain-containing protein
  • TmpF
KeywordsVIRUS / bacteriophage / phage / contractile / phi812 / baseplate
Function / homology
Function and homology information


Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / Protein of unknown function DUF2634 / Protein of unknown function (DUF2634) / Baseplate protein J-like / Baseplate J-like protein / LysM domain superfamily / LysM domain
Similarity search - Domain/homology
Baseplate wedge subunit / Baseplate component / TmpF / DUF4815 domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBinovsky, J. / Siborova, M. / Baska, R. / Pichel-Beleiro, A. / Skubnik, K. / Novacek, J. / van Raaij, M.J. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 2items
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. / Baska, R. / Pichel-Beleiro, A. / Skubnik, K. / Novacek, J. / van Raaij, M.J. / Plevka, P.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baseplate wedge subunit
B: Baseplate component
C: Baseplate component
D: TmpF
E: DUF4815 domain-containing protein
F: DUF4815 domain-containing protein
G: DUF4815 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)609,2907
Polymers609,2907
Non-polymers00
Water00
1
A: Baseplate wedge subunit
B: Baseplate component
C: Baseplate component
D: TmpF
E: DUF4815 domain-containing protein
F: DUF4815 domain-containing protein
G: DUF4815 domain-containing protein

A: Baseplate wedge subunit
B: Baseplate component
C: Baseplate component
D: TmpF
E: DUF4815 domain-containing protein
F: DUF4815 domain-containing protein
G: DUF4815 domain-containing protein

A: Baseplate wedge subunit
B: Baseplate component
C: Baseplate component
D: TmpF
E: DUF4815 domain-containing protein
F: DUF4815 domain-containing protein
G: DUF4815 domain-containing protein

A: Baseplate wedge subunit
B: Baseplate component
C: Baseplate component
D: TmpF
E: DUF4815 domain-containing protein
F: DUF4815 domain-containing protein
G: DUF4815 domain-containing protein

A: Baseplate wedge subunit
B: Baseplate component
C: Baseplate component
D: TmpF
E: DUF4815 domain-containing protein
F: DUF4815 domain-containing protein
G: DUF4815 domain-containing protein

A: Baseplate wedge subunit
B: Baseplate component
C: Baseplate component
D: TmpF
E: DUF4815 domain-containing protein
F: DUF4815 domain-containing protein
G: DUF4815 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)3,655,74142
Polymers3,655,74142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
MethodUCSF CHIMERA

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Components

#1: Protein Baseplate wedge subunit / sheath initiator protein


Mass: 26611.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1UXD7
#2: Protein Baseplate component / wedge protein


Mass: 39248.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1WF63
#3: Protein TmpF / arm scaffold protein


Mass: 116391.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1WGD3
#4: Protein DUF4815 domain-containing protein / tripod protein


Mass: 129262.961 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A8E5NSA0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Staphylococcus phage 812VIRUSall0NATURAL
2TailCOMPLEXall1NATURAL
3BaseplateCOMPLEXall2NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Staphylococcus phage 812 (virus)307898
32Staphylococcus phage 812 (virus)307898
43Staphylococcus phage 812 (virus)307898
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 8 / Details: 50mM Tris, 10mM NaCl, 10mM CaCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 7 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 15371
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF ChimeraXmodel fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
12RELION43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 54841
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25203 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005181794
ELECTRON MICROSCOPYf_angle_d0.755246444
ELECTRON MICROSCOPYf_dihedral_angle_d23.60767704
ELECTRON MICROSCOPYf_chiral_restr0.05627702
ELECTRON MICROSCOPYf_plane_restr0.0132172

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