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- PDB-9tio: Phage 812 baseplate in the pre-contraction state - upper arm (seg... -

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Basic information

Entry
Database: PDB / ID: 9tio
TitlePhage 812 baseplate in the pre-contraction state - upper arm (segment B)
Components
  • CBM-cenC domain-containing protein
  • ORF63
  • ORF64
  • ORF65
KeywordsVIRUS / phage / baseplate
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds
Similarity search - Function
Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / Carbohydrate-binding, CenC-like / Carbohydrate binding domain
Similarity search - Domain/homology
CBM-cenC domain-containing protein / ORF65 / ORF64 / ORF63
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBinovsky, 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: Conformational changes of baseplate regulating tail contraction of Staphylococcus phage 812
Authors: Binovsky, J. / Plevka, P.
History
DepositionDec 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data 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: ORF65
B: ORF65
C: ORF64
D: ORF65
E: ORF64
F: ORF64
G: ORF63
H: CBM-cenC domain-containing protein
I: CBM-cenC domain-containing protein
J: CBM-cenC domain-containing protein
K: ORF64


Theoretical massNumber of molelcules
Total (without water)799,18211
Polymers799,18211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ORF65


Mass: 129262.961 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: tripod protein / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q2
#2: Protein
ORF64


Mass: 19259.613 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: arm segment protein / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q3
#3: Protein ORF63


Mass: 116389.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arm scaffold protein / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q4
#4: Protein CBM-cenC domain-containing protein


Mass: 72654.742 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: receptor-binding protein 1 / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: A0A0U1UXW5
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

ComponentName: Staphylococcus phage 812K1/420 / Type: VIRUS
Details: Propagated in S. aureus SA 812 (CCM 4028) planktonic culture and purified on a CsCl gradient.
Entity ID: all / Source: NATURAL
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtrisTris1
210 mMsodium chlorideNaCl1
310 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10e9 PFU/ml
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 26731

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF ChimeraX1.9model fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 64874
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19727 / Symmetry type: POINT
Atomic model buildingB value: 28.5 / Protocol: FLEXIBLE FIT / Space: REAL

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