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- PDB-9fko: Arm segment of bacteriophage phi812 -

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Basic information

Entry
Database: PDB / ID: 9fko
TitleArm segment of bacteriophage phi812
Components
  • Baseplate protein
  • Unknown peptide
KeywordsVIRUS / phage / arm segment
Function / homology: / Baseplate wedge 3 tail fiber network component / Baseplate protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsSiborova, M. / Baska, R. / Binovsky, J. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
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
DepositionJun 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baseplate protein
B: Baseplate protein
C: Baseplate protein
D: Baseplate protein
E: Baseplate protein
F: Baseplate protein
G: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)116,6577
Polymers116,6577
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baseplate protein
C: Baseplate protein
F: Baseplate protein
G: Unknown peptide

A: Baseplate protein


Theoretical massNumber of molelcules
Total (without water)77,9765
Polymers77,9765
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
3
D: Baseplate protein

E: Baseplate protein


Theoretical massNumber of molelcules
Total (without water)38,6812
Polymers38,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y+1/2,-z+21
Buried area2600 Å2
ΔGint-19 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.930, 75.140, 94.450
Angle α, β, γ (deg.)90.000, 109.870, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Baseplate protein


Mass: 19340.623 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 812 (virus)
Gene: 812_119, 812_121, 812a_121, 812F1_121, K1/420_121, K1_121
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1WGQ5
#2: Protein/peptide Unknown peptide


Mass: 613.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.98 % / Description: thick needles
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M LiCl, 0.1 M Tris (pH=7.5), 25 % w/v PEG 4 000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.8233 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2018
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8233 Å / Relative weight: 1
ReflectionResolution: 1.797→46.49 Å / Num. obs: 109412 / % possible obs: 96.07 % / Redundancy: 2.6 % / Biso Wilson estimate: 38.12 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 3.04
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 8201

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→46.49 Å / SU ML: 0.294 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2753 5471 5 %
Rwork0.2452 103940 -
obs0.2467 109411 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8184 0 35 20 8239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01128392
X-RAY DIFFRACTIONf_angle_d1.146311416
X-RAY DIFFRACTIONf_chiral_restr0.06621303
X-RAY DIFFRACTIONf_plane_restr0.01231470
X-RAY DIFFRACTIONf_dihedral_angle_d7.3041110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.42921120.44312133X-RAY DIFFRACTION59.23
1.82-1.840.40821450.37392763X-RAY DIFFRACTION77.28
1.84-1.860.38611530.34132895X-RAY DIFFRACTION80.76
1.86-1.890.36091620.31843088X-RAY DIFFRACTION85.8
1.89-1.910.33291690.29863213X-RAY DIFFRACTION90.16
1.91-1.940.33141790.29423404X-RAY DIFFRACTION94.09
1.94-1.960.32051830.29523470X-RAY DIFFRACTION97.08
1.96-1.990.33511870.31273545X-RAY DIFFRACTION98.86
1.99-2.020.36971880.33153570X-RAY DIFFRACTION99.16
2.02-2.060.36451870.3133562X-RAY DIFFRACTION99.52
2.06-2.090.29871890.29823589X-RAY DIFFRACTION99.84
2.09-2.130.35541870.29513559X-RAY DIFFRACTION100
2.13-2.170.34021910.28973617X-RAY DIFFRACTION100
2.17-2.220.32431910.28633635X-RAY DIFFRACTION100
2.22-2.260.31571880.273574X-RAY DIFFRACTION100
2.26-2.320.29091870.27413549X-RAY DIFFRACTION100
2.32-2.370.31021900.27783622X-RAY DIFFRACTION100
2.38-2.440.32361910.29013622X-RAY DIFFRACTION100
2.44-2.510.32871900.29843613X-RAY DIFFRACTION100
2.51-2.590.33681880.29573574X-RAY DIFFRACTION100
2.59-2.680.33081910.28463629X-RAY DIFFRACTION100
2.68-2.790.33671900.29553606X-RAY DIFFRACTION100
2.79-2.920.31381890.29323594X-RAY DIFFRACTION100
2.92-3.070.33391900.29743602X-RAY DIFFRACTION100
3.07-3.270.33211920.27713650X-RAY DIFFRACTION100
3.27-3.520.28931890.25613596X-RAY DIFFRACTION100
3.52-3.870.24391920.2153635X-RAY DIFFRACTION100
3.87-4.430.21081920.17863654X-RAY DIFFRACTION100
4.43-5.580.17441910.16053634X-RAY DIFFRACTION99.97
5.58-46.490.19521980.18763743X-RAY DIFFRACTION99.82

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