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- PDB-9tir: Phage 812 baseplate in the post-contraction state (C6) -

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Basic information

Entry
Database: PDB / ID: 9tir
TitlePhage 812 baseplate in the post-contraction state (C6)
Components
  • ORF49
  • ORF61
  • ORF62
  • ORF63
  • ORF64
  • ORF65
  • ORF68
KeywordsVIRUS / phage / baseplate
Function / homology
Function and homology information


: / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / Baseplate protein J-like / Baseplate J-like protein barrel domain ...: / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / Protein of unknown function DUF2634 / Contractile injection system sheath initiator / Baseplate protein J-like / Baseplate J-like protein barrel domain / LysM domain superfamily / LysM domain
Similarity search - Domain/homology
ORF68 / ORF65 / ORF64 / ORF63 / ORF62 / ORF61 / ORF49
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsBinovsky, J. / Plevka, P.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103
CitationJournal: To Be Published
Title: Conformational changes of baseplate linked to tail contraction of S. aureus phage 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: ORF61
B: ORF62
C: ORF62
D: ORF63
E: ORF64
F: ORF64
G: ORF64
H: ORF64
I: ORF64
J: ORF64
K: ORF65
L: ORF65
M: ORF65
N: ORF65
O: ORF65
P: ORF65
Q: ORF68
R: ORF68
S: ORF68
T: ORF49
U: ORF49
V: ORF49
W: ORF49
X: ORF49
Y: ORF49


Theoretical massNumber of molelcules
Total (without water)1,651,41125
Polymers1,651,41125
Non-polymers00
Water00
1
A: ORF61
B: ORF62
C: ORF62
D: ORF63
E: ORF64
F: ORF64
G: ORF64
H: ORF64
I: ORF64
J: ORF64
K: ORF65
L: ORF65
M: ORF65
N: ORF65
O: ORF65
P: ORF65
Q: ORF68
R: ORF68
S: ORF68
T: ORF49
U: ORF49
V: ORF49
W: ORF49
X: ORF49
Y: ORF49
x 6


Theoretical massNumber of molelcules
Total (without water)9,908,467150
Polymers9,908,467150
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

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Protein , 7 types, 25 molecules ABCDEFGHIJKLMNOPQRSTUVWXY

#1: Protein ORF61


Mass: 26611.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q6
#2: Protein ORF62 / Putative baseplate protein


Mass: 39248.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q5
#3: 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
#4: Protein
ORF64


Mass: 19259.613 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q3
#5: 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
#6: 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
#7: Protein
ORF49 / Putative tail sheath protein


Mass: 64559.008 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7R8

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Details

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 / 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: TFS 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: 2400 nm / Nominal defocus min: 1000 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
12RELION53D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 54841
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21264 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Fitting of previously refined sub-models (e.g. arm, core and wedge modules, baseplate-proximal tail) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body ...Details: Fitting of previously refined sub-models (e.g. arm, core and wedge modules, baseplate-proximal tail) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (all chains as a single rigid body).

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