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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
ComponentsMajor head protein
KeywordsVIRUS / phi29 / capsid / icosahedral virus capsid / hk97 fold / phage / bacterial immuno-globulin / BIG2 / Icosahedral virus
Biological speciesBacillus phage phi29 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsMorais, M.C. / Choi, K.H. / Koti, J.S. / Chipman, P.R. / Anderson, D.L. / Rossmann, M.G.
CitationJournal: Mol Cell / Year: 2005
Title: Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
Authors: Marc C Morais / Kyung H Choi / Jaya S Koti / Paul R Chipman / Dwight L Anderson / Michael G Rossmann /
Abstract: Bacteriophage phi29 is one of the smallest and simplest known dsDNA phages, making it amenable to structural investigations. The three-dimensional structure of a fiberless, isometric variant has been ...Bacteriophage phi29 is one of the smallest and simplest known dsDNA phages, making it amenable to structural investigations. The three-dimensional structure of a fiberless, isometric variant has been determined to 7.9 A resolution by cryo-electron microscopy (cryo-EM), allowing the identification of alpha helices and beta sheets. Their arrangement indicates that the folds of the phi29 and bacteriophage HK97 capsid proteins are similar except for an additional immunoglobulin-like domain of the phi29 protein. An atomic model that incorporates these two domains fits well into the cryo-EM density of the T = 3, fiberless isometric phi29 particle, and cryo-EM structures of fibered isometric and fiberless prolate prohead phi29 particles at resolutions of 8.7 A and 12.7 A, respectively. Thus, phi29 joins the growing number of phages that utilize the HK97 capsid structure, suggesting that this protein fold may be as prevalent in capsids of dsDNA phages as the jelly roll fold is in eukaryotic viruses.
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.5Feb 14, 2024Group: Database references / Derived calculations / Category: database_2 / pdbx_struct_oper_list
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
Remark 999SEQUENCE The authors state that an alignment between the coordinate C-alpha atoms and the sequence ...SEQUENCE 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
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  • Simplified surface model + fitted atomic model
  • EMDB-1120
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  • Superimposition on EM map
  • EMDB-1120
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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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
Polymers91,9673
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
Polymers5,518,020180
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 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
Polymers459,83515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers551,80218
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: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Major head protein / Late protein Gp8 / Coordinate model: Cα atoms only


Mass: 30655.668 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Cell line: phi29 / Gene: 8 / Production host: Bacillus subtilis (bacteria)

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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: 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 ...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 (virus)
Details of virusHost category: BACTERIA / Type: VIRION
Natural hostOrganism: Bacillus subtilus
Buffer solutionName: tris-HCLTris / pH: 7.8 / Details: tris-HCL
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

MicroscopyModel: FEI/PHILIPS CM200FEG/ST
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
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
4EM3DR3D reconstruction
5PFT3D reconstructionEMPFT
6POR3D reconstruction
CTF correctionDetails: Inverse of CTF was applied to images. Both phases and amplitudes were corrected.
SymmetryPoint symmetry: I (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 ...Method: 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 / Num. of particles: 5922 / Nominal pixel size: 1.8421 Å
Details: Software used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / 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.
Details: METHOD--6D search for each symmetry related molecule in the icosahedral asymmetric unit REFINEMENT PROTOCOL--rigid body
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 0 0 1080

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