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- PDB-9tim: Phage 812 baseplate in the pre-contraction state - upper arm -

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Basic information

Entry
Database: PDB / ID: 9tim
TitlePhage 812 baseplate in the pre-contraction state - upper arm
Components
  • CBM-cenC domain-containing protein
  • ORF63
  • ORF64
  • ORF65
  • ORF68
KeywordsVIRUS / phage / baseplate
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds
Similarity search - Function
: / ORF68-like, C-terminal domain / 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 / ORF68 / ORF65 / ORF64 / ORF63
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 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: ORF63
B: ORF64
C: ORF64
D: ORF64
E: ORF64
F: ORF64
G: ORF64
H: ORF64
I: ORF64
J: ORF64
K: ORF64
L: ORF64
M: ORF64
N: ORF65
O: ORF65
P: ORF65
Q: ORF65
R: ORF65
S: ORF65
T: ORF68
U: ORF68
V: ORF68
W: CBM-cenC domain-containing protein
X: CBM-cenC domain-containing protein
Y: CBM-cenC domain-containing protein


Theoretical massNumber of molelcules
Total (without water)1,492,47025
Polymers1,492,47025
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 ORF63


Mass: 116389.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q4
#2: Protein
ORF64


Mass: 19259.613 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q3
#3: Protein
ORF65


Mass: 129262.961 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q2
#4: Protein ORF68 / Putative receptor binding protein


Mass: 50474.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7P9
#5: Protein CBM-cenC domain-containing protein


Mass: 72654.742 Da / Num. of mol.: 3 / Source method: isolated from a natural source / 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: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19727 / Symmetry type: POINT
Atomic model buildingB value: 132.6 / Protocol: RIGID BODY FIT / Space: REAL
Details: Fitting of previously refined sub-models (e.g. segment A, segment B, segment CDEF from the upper arm) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body ...Details: Fitting of previously refined sub-models (e.g. segment A, segment B, segment CDEF from the upper arm) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (rigid bodies selected: res. 95-472 of arm scaffold protein and dimers of arm segments A, B and C, dimer of arm segment D, dimer of arm segment E, dimer of arm segment F, trimer of tripod proteins, trimer of RBP1, trimer of RBP2, res. 489-752 of arm scaffold protein).

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