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- PDB-4bx4: Fitting of the bacteriophage Phi8 P1 capsid protein into cryo-EM ... -

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Basic information

Entry
Database: PDB / ID: 4bx4
TitleFitting of the bacteriophage Phi8 P1 capsid protein into cryo-EM density
ComponentsP1
KeywordsVIRUS / BACTERIOPHAGE
Function / homology: / Major inner capsid protein P1 / identical protein binding / p1
Function and homology information
Biological speciesPSEUDOMONAS PHAGE PHI8 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsEl Omari, K. / Sutton, G. / Ravantti, J.J. / Zhang, H. / Walter, T.S. / Grimes, J.M. / Bamford, D.H. / Stuart, D.I. / Mancini, E.J.
CitationJournal: Structure / Year: 2013
Title: Plate tectonics of virus shell assembly and reorganization in phage φ8, a distant relative of mammalian reoviruses.
Authors: Kamel El Omari / Geoff Sutton / Janne J Ravantti / Hanwen Zhang / Thomas S Walter / Jonathan M Grimes / Dennis H Bamford / David I Stuart / Erika J Mancini /
Abstract: The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein ...The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein multiplicity (120 copies) to form their closed capsids. We have determined the atomic structure of the capsid protein (P1) from the dsRNA cystovirus Φ8. In the crystal P1 forms pentamers, very similar in shape to facets of empty procapsids, suggesting an unexpected assembly pathway that proceeds via a pentameric intermediate. Unlike the elongated proteins used by dsRNA mammalian reoviruses, P1 has a compact trapezoid-like shape and a distinct arrangement in the shell, with two near-identical conformers in nonequivalent structural environments. Nevertheless, structural similarity with the analogous protein from the mammalian viruses suggests a common ancestor. The unusual shape of the molecule may facilitate dramatic capsid expansion during phage maturation, allowing P1 to switch interaction interfaces to provide capsid plasticity.
History
DepositionJul 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Other
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1300
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  • Superimposition on EM map
  • EMDB-1300
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P1
B: P1


Theoretical massNumber of molelcules
Total (without water)173,9422
Polymers173,9422
Non-polymers00
Water0
1
A: P1
B: P1
x 60


Theoretical massNumber of molelcules
Total (without water)10,436,529120
Polymers10,436,529120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: P1
B: P1
x 5


  • icosahedral pentamer
  • 870 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)869,71110
Polymers869,71110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: P1
B: P1
x 6


  • icosahedral 23 hexamer
  • 1.04 MDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)1,043,65312
Polymers1,043,65312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
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))
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein P1


Mass: 86971.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI8 (bacteriophage) / Plasmid: PDK5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9MC13

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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: PSEUDOMONAS PHAGE PHI8 / Type: VIRUS
Buffer solutionName: 10 MM POTASSIUM PHOSPHATE PH7.5, 1 MM MGCL2, 50 MM NACL
pH: 7.5
Details: 10 MM POTASSIUM PHOSPHATE PH7.5, 1 MM MGCL2, 50 MM NACL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 49300 X / Nominal defocus max: 3300 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 66

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Processing

EM software
IDNameVersionCategory
1VEDAmodel fitting
2EM3DR23D reconstruction
3P3DR3D reconstruction
4PFT23D reconstruction
5POR3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 8.7 Å / Num. of particles: 12867 / Details: COORDINATES FITTED TO CRYO-EM MAP EMD-1300 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 4BTP

4btp

RefinementHighest resolution: 8.7 Å
Refinement stepCycle: LAST / Highest resolution: 8.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11384 0 0 0 11384

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