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- PDB-9rox: Asymmetric unit of bacteriophage 812 prohead II with the complete... -

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Basic information

Entry
Database: PDB / ID: 9rox
TitleAsymmetric unit of bacteriophage 812 prohead II with the complete set of minor capsid proteins
Components
  • Major capsid protein
  • Putative Ig-like protein
  • Virion component
KeywordsVIRUS / Bacterophage / phage cycle / capsid assembly / single particle analysis / the HK97 fold / Herelleviridae
Function / homology: / : / Major capsid protein
Function and homology information
Biological speciesStaphylococcus phage 812K1/420 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsZlatohurska, M. / Prochazkova, M. / Cienikova, Z. / Fuzik, T. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 4items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.01.01/00/22_008/0004607 Czech Republic
European Research Council (ERC)1233487European Union
CitationJournal: To Be Published
Title: Cryo-ET of S. aureus infection by Herelleviridae phage 812
Authors: Zlatohurska, M. / Prochazkova, M. / Cienikova, Z. / Fuzik, T. / Bardy, P. / Pantucek, R. / Plevka, P.
History
DepositionJun 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 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: Putative Ig-like protein
B: Major capsid protein
C: Virion component
D: Major capsid protein
E: Putative Ig-like protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Putative Ig-like protein
L: Major capsid protein
M: Major capsid protein
N: Major capsid protein
O: Putative Ig-like protein
P: Putative Ig-like protein
Q: Major capsid protein
R: Major capsid protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
W: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)881,16622
Polymers881,16622
Non-polymers00
Water00
1
A: Putative Ig-like protein
B: Major capsid protein
C: Virion component
D: Major capsid protein
E: Putative Ig-like protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Putative Ig-like protein
L: Major capsid protein
M: Major capsid protein
N: Major capsid protein
O: Putative Ig-like protein
P: Putative Ig-like protein
Q: Major capsid protein
R: Major capsid protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
W: Major capsid protein
x 61


Theoretical massNumber of molelcules
Total (without water)53,751,1171342
Polymers53,751,1171342
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Putative Ig-like protein


Mass: 19624.799 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: A0A0U1UYD0
#2: Protein
Major capsid protein


Mass: 48446.559 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: A1YTN4
#3: Protein Virion component


Mass: 7896.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: A0A0U1WYT8
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
IDNameTypeDetails (eV)Entity IDParent-IDSource
1Staphylococcus phage 812K1/420VIRUSSingle particle analysis of capsid-like structures from the infected S. aureus cellsall0NATURAL
2The asymmetric unit of bacteriophage 812 prohead II with the complete set of minor capsid proteinsCOMPLEXall1NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Staphylococcus phage 812K1/420 (virus)3434241
32Staphylococcus phage 812K1/420 (virus)3434241
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Staphylococcus aureus / Strain: 1137
Virus shellName: capsid / Diameter: 1040 nm / Triangulation number (T number): 16
Buffer solutionpH: 7.5
Details: Phage buffer, adjusted by Tris-HCl (pH 8) to a final pH of approx. 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMsodium chlorideNaCl1
210 mMcalcium chlorideCaCl21
350 mMTris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K / Details: One-side blotting

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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: 81000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 21755

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Processing

EM software
IDNameVersionCategory
1crYOLO1.8.3particle selection
2SerialEMimage acquisition
7Coot0.9.4.1.ELmodel fitting
9RELION5.0betainitial Euler assignment
10RELION5.0betafinal Euler assignment
11RELION5.0betaclassification
12RELION5.0beta3D reconstruction
19PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 68779
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20569 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 5LII

5lii


Accession code: 5LII / Source name: PDB / Type: experimental model

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