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- PDB-9f04: Cryo-EM structure of Staphylococcus aureus bacteriophage phi812 t... -

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Basic information

Entry
Database: PDB / ID: 9f04
TitleCryo-EM structure of Staphylococcus aureus bacteriophage phi812 tail in the pre-contraction state - tube and sheath proteins
Components
  • Capsid protein
  • Major tail sheath protein
KeywordsVIRUS / bacteriophage / phage / contractile / phi812 / tail
Function / homologyMajor tail sheath protein / Capsid protein
Function and homology information
Biological speciesStaphylococcus phage 812 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBinovsky, J. / Siborova, M. / Skubnik, K. / Novacek, 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: Cell attachment and tail contraction of S. aureus phage phi812
Authors: Binovsky, J. / Siborova, M. / Skubnik, K. / Novacek, J. / Plevka, P.
History
DepositionApr 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Major tail sheath protein
F: Major tail sheath protein
H: Major tail sheath protein
E: Major tail sheath protein
D: Capsid protein
C: Capsid protein
B: Capsid protein
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)322,0088
Polymers322,0088
Non-polymers00
Water00
1
G: Major tail sheath protein
F: Major tail sheath protein
H: Major tail sheath protein
E: Major tail sheath protein
D: Capsid protein
C: Capsid protein
B: Capsid protein
A: Capsid protein

G: Major tail sheath protein
F: Major tail sheath protein
H: Major tail sheath protein
E: Major tail sheath protein
D: Capsid protein
C: Capsid protein
B: Capsid protein
A: Capsid protein

G: Major tail sheath protein
F: Major tail sheath protein
H: Major tail sheath protein
E: Major tail sheath protein
D: Capsid protein
C: Capsid protein
B: Capsid protein
A: Capsid protein

G: Major tail sheath protein
F: Major tail sheath protein
H: Major tail sheath protein
E: Major tail sheath protein
D: Capsid protein
C: Capsid protein
B: Capsid protein
A: Capsid protein

G: Major tail sheath protein
F: Major tail sheath protein
H: Major tail sheath protein
E: Major tail sheath protein
D: Capsid protein
C: Capsid protein
B: Capsid protein
A: Capsid protein

G: Major tail sheath protein
F: Major tail sheath protein
H: Major tail sheath protein
E: Major tail sheath protein
D: Capsid protein
C: Capsid protein
B: Capsid protein
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)1,932,04748
Polymers1,932,04748
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
MethodUCSF CHIMERA

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Components

#1: Protein
Major tail sheath protein / tail sheath protein


Mass: 64559.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A0A0U1WZ79
#2: Protein
Capsid protein / tail tube protein


Mass: 15942.970 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / References: UniProt: A1YTP2
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

Component
IDNameTypeEntity IDParent-IDSource
1Staphylococcus phage 812VIRUSall0NATURAL
2TailCOMPLEXall1NATURAL
3Tail tubeCOMPLEX#22NATURAL
4Tail sheathCOMPLEX#12NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Staphylococcus phage 812 (virus)307898
32Staphylococcus phage 812 (virus)307898
43Staphylococcus phage 812 (virus)307898
54Staphylococcus phage 812 (virus)307898
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NONOSPECIESVIRION
22
33
44
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 1 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 18

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Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
2EPUimage acquisition
8PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18188 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005127800
ELECTRON MICROSCOPYf_angle_d0.72172536
ELECTRON MICROSCOPYf_dihedral_angle_d24.3947688
ELECTRON MICROSCOPYf_chiral_restr0.05319416
ELECTRON MICROSCOPYf_plane_restr0.00622560

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