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- PDB-3jb5: Capsid Structure of the Propionibacterium acnes Bacteriophage ATC... -

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Basic information

Entry
Database: PDB / ID: 3jb5
TitleCapsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear
Componentsmajor capsid protein
KeywordsVIRUS / acne / bacteriophage / HK97-like
Function / homologyGp6
Function and homology information
Biological speciesPropionibacterium phage PA6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChiou, J. / Zhang, X. / Marinelli, L.J. / Modlin, R.L. / Zhou, Z.H.
CitationJournal: To be Published
Title: Capsid Structure of the Propionibacterium acnes Bacteriophage ATCC_Clear
Authors: Chiou, J. / Zhang, X. / Marinelli, L.J. / Modlin, R.L. / Zhou, Z.H.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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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-6398
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein


Theoretical massNumber of molelcules
Total (without water)229,3567
Polymers229,3567
Non-polymers00
Water0
1
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)13,761,334420
Polymers13,761,334420
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
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
x 5


  • icosahedral pentamer
  • 1.15 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,146,77835
Polymers1,146,77835
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: major capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.38 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,376,13342
Polymers1,376,13342
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
major capsid protein


Mass: 32765.082 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Propionibacterium phage PA6 (virus) / References: UniProt: A4K473

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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: Propionibacterium acnes bacteriophage ATCC_Clear / Type: VIRUS
Molecular weightValue: 33 MDa / Experimental value: YES
Details of virusEmpty: NO / Enveloped: NO / Host category: BACTERIA(EUBACTERIA) / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Propionibacterium acnes / Strain: 6919
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Purified sample was applied to a Quantifoil grid.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 15 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Method: Blot for 15 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 16, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38462 X / Calibrated magnification: 38462 X / Nominal defocus max: 2270 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 3168
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: FREALIGN / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27504 / Nominal pixel size: 1.3 Å / Actual pixel size: 1.3 Å
Details: (Single particle details: The particles were selected using an in-house selection procedure.) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms15232 0 0 0 15232

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