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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 / Virus
Specimen sourceBacillus phage phi29 / virus / image: Bacillus subtilis
MethodElectron microscopy (7.9 Å resolution / Particle / Single particle)
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 22, 2005 / Release: Apr 26, 2005
RevisionDateData content typeGroupProviderType
1.0Apr 26, 2005Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
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)91,9673
Polyers91,9673
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)5,518,020180
Polyers5,518,020180
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)459,83515
Polyers459,83515
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)551,80218
Polyers551,80218
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

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Components

#1: Polypeptide(L)Major head protein / Late protein Gp8 / Coordinate model: Cα atoms only


Mass: 30655.668 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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Fiberless isometric phi29 capsid / Type: VIRUS
Details: The capsid protein assembles a T=3 icosahedral virus shell. 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:
Source: NATURAL
Source (natural)Organism: Enterobacteria phage T4
Details of virusVirus host category: BACTERIA / Virus type: VIRION
Natural hostOrganism: Bacillus subtilus
Buffer solutionName: tris-HCL / Details: tris-HCL / pH: 7.8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: electron microscopy grid - in vitreous ice
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: frozen in liquid ethane

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG/ST
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 100 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
1EMFitMODEL FITTING
2SITUS COLORESMODEL FITTING
3SITUS COLORESMODEL FITTING
4EM3DRRECONSTRUCTION
5PFTRECONSTRUCTIONEMPFT
6PORRECONSTRUCTION
CTF correctionDetails: Inverse of CTF was applied to images. Both phases and amplitudes were corrected.
SymmetryPoint symmetry: I
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 Å / Number of particles: 5922 / Nominal pixel size: 1.8421
Details: Software used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--6D search for each symmetry related molecule in the icosahedral asymmetric unit REFINEMENT PROTOCOL--rigid body
Ref protocol: RIGID BODY FIT / 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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