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- PDB-6ib1: Icosahedrally averaged capsid of empty particle of bacteriophage P68 -

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Basic information

Entry
Database: PDB / ID: 6ib1
TitleIcosahedrally averaged capsid of empty particle of bacteriophage P68
Components
  • Major head protein
  • Uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / bacteriophage capsid / HK97 fold
Function / homologyUncharacterized protein / Major head protein
Function and homology information
Biological speciesStaphylococcus phage P68 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHrebik, D. / Skubnik, K. / Fuzik, T. / Plevka, P.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization3041 Czech Republic
16-29916A Czech Republic
CitationJournal: Sci Adv / Year: 2019
Title: Structure and genome ejection mechanism of phage P68.
Authors: Dominik Hrebík / Dana Štveráková / Karel Škubník / Tibor Füzik / Roman Pantůček / Pavel Plevka /
Abstract: Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect ...Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.
History
DepositionNov 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-4442
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  • Superimposition on EM map
  • EMDB-4442
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Structure viewerMolecule:
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Assembly

Deposited unit
C: Major head protein
D: Major head protein
B: Major head protein
A: Major head protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)215,5108
Polymers215,5108
Non-polymers00
Water00
1
C: Major head protein
D: Major head protein
B: Major head protein
A: Major head protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
x 60


Theoretical massNumber of molelcules
Total (without water)12,930,577480
Polymers12,930,577480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Major head protein
D: Major head protein
B: Major head protein
A: Major head protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
x 5


  • icosahedral pentamer
  • 1.08 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,077,54840
Polymers1,077,54840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
C: Major head protein
D: Major head protein
B: Major head protein
A: Major head protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
x 6


  • icosahedral 23 hexamer
  • 1.29 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,293,05848
Polymers1,293,05848
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein
Major head protein


Mass: 46954.941 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I3
#2: Protein
Uncharacterized protein


Mass: 6922.464 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: MYEGNNMRSMMGTSYEDSRLNKRTELNENMSIDTNKSEDSYGVQIHSLSKQSFTGDVEEE
Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I2

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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 P68VIRUSall0NATURAL
2Major capsid proteinCOMPLEX#11NATURAL
3Arstotzka proteinCOMPLEX#21NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
1119.7 MDaNO
210.047 MDaNO
310.0069 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Staphylococcus phage P68 (virus)204090
32Staphylococcus phage P68 (virus)204090
43Staphylococcus phage P68 (virus)204090
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NONOSTRAINVIRION
22
33
Natural host
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Staphylococcus aureus1280dTarM 4220
12
13
Virus shell
IDEntity assembly-IDNameDiameter (nm)Triangulation number (T number)
11Capsid4804
12
13
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethaneTris1
210 mMcalcium chlorideCaCl1
310 mMsodium chlorideNaCl1
SpecimenConc.: 2 mg/ml / Embedding 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: 293 K / Details: blot time 2s; blot force -2; 3.6 ul of sample

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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: 3 nm / Nominal defocus min: 1 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 21 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2891
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

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Processing

EM software
IDNameVersionCategory
1EMAN22.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.8.8model fitting
9PHENIXdev:3042model refinement
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10259 / Details: Manual selection in EMAN
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8580 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Details: Reconstruction of the native P68 capsid was used as initial model
Atomic model buildingPDB-ID: 6IAT

6iat


Accession code: 6IAT / Source name: PDB / Type: experimental model

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