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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: EMBO J / Year: 2026
Title: Conformational changes of the baseplate regulating tail contraction of Staphylococcus phage 812.
Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos ...Authors: Ján Bíňovský / Marta Šiborová / Maryna Zlatohurska / Jiří Nováček / Pavol Bárdy / Roman Baška / Karel Škubník / Tibor Botka / Martin Benešík / Roman Pantůček / Konstantinos Tripsianes / Pavel Plevka /
Abstract: Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of ...Phages with contractile tails employ elaborate mechanisms to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Here, we used cryo-EM to show that the baseplate of phage 812, a member of the Kayvirus genus, which infects Gram-positive Staphylococcus strains, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins 1 and 2 and tripod complexes. Upon binding to a host cell, the receptor-binding proteins of phage 812 baseplate reorient and undergo conformational changes. The changes to the tripod complexes trigger the release of the central spike and weld proteins, which expose peptidoglycan-degrading domains of the hub proteins. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring of the tail sheath initiator proteins expands and triggers the contraction of the tail sheath, which shortens to 50% and pushes the tail tube 10-30 nm into the bacterial cytoplasm. Homologous molecular mechanisms are probably shared by phages of the Herelleviridae family with contractile tails to infect Gram-positive bacteria.
History
DepositionDec 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: 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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