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- PDB-1yxn: Pseudo-atomic model of a fiberless isometric variant of bacteriop... -

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Basic information

Entry
Database: PDB / ID: 1yxn
TitlePseudo-atomic model of a fiberless isometric variant of bacteriophage phi29
DescriptorMajor head protein
KeywordsVirus / phi29 / capsid / icosahedral virus capsid / hk97 fold / phage / bacterial immuno-globulin / BIG2 / Icosahedral virus
Specimen sourceBacillus phage phi29 / virus / image: Bacillus subtilis
MethodElectron microscopy (7.9 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsMorais, M.C. / Choi, K.H. / Koti, J.S. / Chipman, P.R. / Anderson, D.L. / Rossmann, M.G.
CitationMol. Cell, 2005, 18, 149-159

Mol. Cell, 2005, 18, 149-159 StrPapers
Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
Marc C Morais / Kyung H Choi / Jaya S Koti / Paul R Chipman / Dwight L Anderson / Michael G Rossmann

DateDeposition: Feb 22, 2005 / Release: Apr 26, 2005 / Last modification: Feb 24, 2009
Remark 999SEQUENCE The authors state that an alignment between the coordinate C-alpha atoms and the sequence is not possible. The following is the one-letter sequence for the protein modeled in this structure, SwissProt entry P13849: MRITFNDVKTSLGITESYDIVNAIRNSQGDNFKSYVPLATANNVAEVGAGILINQTVQND FITSLVDRIGLVVIRQVSLNNPLKKFKKGQIPLGRTIEEIYTDITKEKQYDAEEAEQKVF EREMPNVKTLFHERNRQGFYHQTIQDDSLKTAFVSWGNFESFVSSIINAIYNSAEVDEYE YMKLLVDNYYSKGLFTTVKIDEPTSSTGALTEFVKKMRATARKLTLPQGSRDWNSMAVRT RSYMEDLHLIIDADLEAELDVDVLAKAFNMNRTDFLGNVTVIDGFASTGLEAVLVDKDWF MVYDNLHKMETVRNPRGLYWNYYYHVWQTLSVSRFANAVAFVSGDVPAVTQVIVSPNIAA VKQGGQQQFTAYVRATNAKDHKVVWSVEGGSTGTAITGDGLLSVSGNEDNQLTVKATVDI GTEDKPKLVVGEAVVSIRPNNASGGAQA

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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-1116
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  • Simplified surface model + fitted atomic model
  • EMDB-1120
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Assembly

Deposited unit
A: Major head protein
B: Major head protein
C: Major head protein


Theoretical massNumber of molelcules
Total (without water)91,9683
Polyers91,9683
Non-polymers00
Water0
#1
A: Major head protein
B: Major head protein
C: Major head protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,518,084180
Polyers5,518,084180
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: Major head protein
B: Major head protein
C: Major head protein
x 5


  • icosahedral pentamer
  • 460 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)459,84015
Polyers459,84015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Major head protein
B: Major head protein
C: Major head protein
x 6


  • icosahedral 23 hexamer
  • 552 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)551,80818
Polyers551,80818
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • 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: Polypeptide(L)Major head protein / Late protein Gp8


Mass: 30656.020 Da / Num. of mol.: 3
Source: (gene. exp.) Bacillus phage phi29 / virus / image: Bacillus subtilis

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: Fiberless isometric phi29 capsid / Aggregation state: PARTICLE
ComponentName: The capsid protein assembles a T=3 icosahedral virus shell.
Details: The virus particle is a protein shell with icosahedral symmetry. To generate the complete icosahedral particle, apply the following 59 matrices to the three chains in the icosahedral asymmetric unit, and combine with the original coordinates of the icosahedral asymmetric unit:
Details of the virusVirus host category: Bacteria / Virus host growth cell: Bacillus subtilus / Virus host species: Bacillus subtilus / Virus type: bacteriophage
Buffer solutionName: tris-HCL
Sample preparationpH: 7.8 / Sample conc.: 1 mg/ml
Specimen supportDetails: electron microscopy grid - in vitreous ice
VitrificationDetails: frozen in liquid ethane

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG/ST
Electron gunElectron source: Field emmission gun / Accelerating voltage: 200 kV
Electron lensNominal magnification: 38000 X / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: KODAK SO163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: Situs (colores)
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: 3D reconstructions were calculated using the Fourier-Bessel method. Initial orientations were found via common-lines, improved using model based polar Fourier transform methods, and finally refined by minimizing the vector difference between between structure factors calculated from a particle image and those from a central section of the Fourier transform of the model.
Resolution: 7.9 A / Nominal pixel size: 1.8421 A/pix
CTF correction method: Inverse of CTF was applied to images. Both phases and amplitudes were corrected.
Details: Software used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement.
Atomic model buildingMethod: 6D search for each symmetry related molecule in the icosahedral asymmetric unit
Software name: Situs (colores) / Ref protocol: rigid body / Ref space: REAL
Target criteria: rigid body refinement in real space against laplacian filtered EM density, using the program COLORES in the package SITUS. Each molecule in the T=3 asymmetric unit was refined separately.
Number of atoms included #LASTProtein: 1080 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1080

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