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- PDB-3j1a: HK97-like fold fitted into 3D reconstruction of bacteriophage CW02 -

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Basic information

Entry
Database: PDB / ID: 3j1a
TitleHK97-like fold fitted into 3D reconstruction of bacteriophage CW02
Componentscapsid proteinCapsid
KeywordsVIRUS / halophage / bacteriophage HK97 / bacteriophage T7 / T7-like phage / turret / extremophile / Great Salt Lake
Function / homologyPhage capsid / Phage capsid family / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesGreat Salt Lake bacteriophage CW02 (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16 Å
AuthorsShen, P.S. / Domek, M.J. / Sanz-Garcia, E. / Makaju, A. / Taylor, R. / Culumber, M. / Breakwell, D.P. / Prince, J.T. / Belnap, D.M.
CitationJournal: J Virol / Year: 2012
Title: Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.
Authors: Peter S Shen / Matthew J Domek / Eduardo Sanz-García / Aman Makaju / Ryan M Taylor / Ryan Hoggan / Michele D Culumber / Craig J Oberg / Donald P Breakwell / John T Prince / David M Belnap /
Abstract: Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, ...Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, mass spectrometry, and electron microscopy. A conserved module of structural genes places CW02 in the T7 supergroup, members of which are found in diverse aquatic environments, including marine and freshwater ecosystems. CW02 has morphological similarities to viruses of the Podoviridae family. The structure of CW02, solved by cryogenic electron microscopy and three-dimensional reconstruction, enabled the fitting of a portion of the bacteriophage HK97 capsid protein into CW02 capsid density, thereby providing additional evidence that capsid proteins of tailed double-stranded DNA phages have a conserved fold. The CW02 capsid consists of bacteriophage lambda gpD-like densities that likely contribute to particle stability. Turret-like densities were found on icosahedral vertices and may represent a unique adaptation similar to what has been seen in other extremophilic viruses that infect archaea, such as Sulfolobus turreted icosahedral virus and halophage SH1.
History
DepositionJan 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: em_image_scans / em_software / struct_ref_seq
Item: _em_software.image_processing_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3Feb 21, 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

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  • 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-5388
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)153,6137
Polymers153,6137
Non-polymers00
Water0
1
A: capsid protein
B: capsid protein
C: capsid protein
D: capsid protein
E: capsid protein
F: capsid protein
G: capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)9,216,764420
Polymers9,216,764420
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: capsid protein
B: capsid protein
C: capsid protein
D: capsid protein
E: capsid protein
F: capsid protein
G: capsid protein
x 5


  • icosahedral pentamer
  • 768 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)768,06435
Polymers768,06435
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid protein
B: capsid protein
C: capsid protein
D: capsid protein
E: capsid protein
F: capsid protein
G: capsid protein
x 6


  • icosahedral 23 hexamer
  • 922 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)921,67642
Polymers921,67642
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
capsid protein / Capsid / HK97 fold / Coordinate model: Cα atoms only


Mass: 21944.676 Da / Num. of mol.: 7 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source
Source: (natural) Great Salt Lake bacteriophage CW02 (others)
References: UniProt: P49861*PLUS
Sequence detailsMODELED SEQUENCE COMPRISES RESIDUES 182-380 OF MAJOR CAPSID PROTEIN FROM ENTEROBACTERIA PHAGE HK97 ...MODELED SEQUENCE COMPRISES RESIDUES 182-380 OF MAJOR CAPSID PROTEIN FROM ENTEROBACTERIA PHAGE HK97 (UNP P49861).

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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: Bacteriophage CW02 / Type: VIRUS
Details: Head and tail phage. Sample buffer solution contains 8% NaCl
Details of virusEmpty: NO / Enveloped: NO / Host category: BACTERIA(EUBACTERIA) / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Salinivibrio costicola
Buffer solutionpH: 8
Details: 1.35 M NaCl, 48 mM MgSO4-7H2O, 1 mM CaCl2, 2 mM Tris-Cl
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 1.35 M NaCl, 48 mM MgSO4-7H2O, 1 mM CaCl2, 2 mM Tris-Cl
Specimen supportDetails: 200 mesh, holey-carbon-coated copper grid
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Blotted for 4 seconds before plunging into liquid ethane (FEI Vitrobot MarK III)
Method: Blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jul 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 39000 X / Calibrated magnification: 37564 X / Nominal defocus max: 2800 nm / Nominal defocus min: 200 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 93 K / Temperature (max): 94 K / Temperature (min): 92 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2EM3DR23D reconstruction
3PFT23D reconstruction
4PFT3DR3D reconstruction
CTF correctionDetails: whole micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 16 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 8695 / Details: Particles were manually selected using X3D / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: REFINEMENT PROTOCOL--Automatic rigid body DETAILS--C-alpha coordinates pertaining to the HK97-fold were separately fitted as rigid bodies into capsid hexamers or pentamers.
Atomic model buildingPDB-ID: 1OHG
Pdb chain-ID: G / Accession code: 1OHG / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 0 0 898

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