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- PDB-3izg: Bacteriophage T7 prohead shell EM-derived atomic model -

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Basic information

Entry
Database: PDB / ID: 3izg
TitleBacteriophage T7 prohead shell EM-derived atomic model
DescriptorMajor capsid protein 10A
KeywordsVIRUS / bacteriophage / virus / capsid maturation / cryoelectron microscopy / morphogenetic intermediate / icosahedral
Specimen sourceEnterobacteria phage T7 / virus / Bacteriophage T7
MethodElectron microscopy (10.9 Å resolution / Particle / Single particle)
AuthorsIonel, A. / Velazquez-Muriel, J.A. / Agirrezabala, X. / Luque, D. / Cuervo, A. / Caston, J.R. / Valpuesta, J.M. / Martin-Benito, J. / Carrascosa, J.L.
CitationJ. Biol. Chem., 2011, 286, 234-242

primary. J. Biol. Chem., 2011, 286, 234-242 Yorodumi Papers
Molecular rearrangements involved in the capsid shell maturation of bacteriophage T7.
Alina Ionel / Javier A Velázquez-Muriel / Daniel Luque / Ana Cuervo / José R Castón / José M Valpuesta / Jaime Martín-Benito / José L Carrascosa

#1. Structure, 2007, 15, 461-472 Yorodumi Papers
Quasi-atomic model of bacteriophage t7 procapsid shell: insights into the structure and evolution of a basic fold.
Agirrezabala, X. / Velazquez-Muriel, J.A. / Gomez-Puertas, P. / Scheres, S.H. / Carazo, J.M. / Carrascosa, J.L.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 27, 2010 / Release: Nov 17, 2010
RevisionDateData content typeGroupProviderType
1.0Nov 17, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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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
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Assembly

Deposited unit
G: Major capsid protein 10A
A: Major capsid protein 10A
B: Major capsid protein 10A
C: Major capsid protein 10A
D: Major capsid protein 10A
E: Major capsid protein 10A
F: Major capsid protein 10A


Theoretical massNumber of molelcules
Total (without water)256,1277
Polyers256,1277
Non-polymers00
Water0
#1
G: Major capsid protein 10A
A: Major capsid protein 10A
B: Major capsid protein 10A
C: Major capsid protein 10A
D: Major capsid protein 10A
E: Major capsid protein 10A
F: Major capsid protein 10A
x 60


Theoretical massNumber of molelcules
Total (without water)15,367,643420
Polyers15,367,643420
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
G: Major capsid protein 10A
A: Major capsid protein 10A
B: Major capsid protein 10A
C: Major capsid protein 10A
D: Major capsid protein 10A
E: Major capsid protein 10A
F: Major capsid protein 10A
x 5


  • icosahedral pentamer
  • 1.28 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,280,63735
Polyers1,280,63735
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
G: Major capsid protein 10A
A: Major capsid protein 10A
B: Major capsid protein 10A
C: Major capsid protein 10A
D: Major capsid protein 10A
E: Major capsid protein 10A
F: Major capsid protein 10A
x 6


  • icosahedral 23 hexamer
  • 1.54 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,536,76442
Polyers1,536,76442
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 capsid protein 10A


Mass: 36589.625 Da / Num. of mol.: 7 / Source: (natural) Enterobacteria phage T7 / virus / References: UniProt: P19726

Cellular component

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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: bacteriophage T7 prohead / Type: VIRUS / Details: gp10A
Details of virusVirus host category: BACTERIA / Virus type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionName: 50mM Tris-HCl pH7.7 10mM MgCl2 100mM NaCl / Details: 50mM Tris-HCl pH7.7 10mM MgCl2 100mM NaCl / pH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 carbon grids
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 51600 / Nominal defocus max: 1000 nm / Nominal defocus min: 3000 nm / Cs: 2.26 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: SPIDER / Category: RECONSTRUCTION
CTF correctionDetails: Wiener filter, defocus groups
SymmetryPoint symmetry: I
3D reconstructionMethod: Spider / Resolution: 10.9 Å / Number of particles: 4460 / Actual pixel size: 2.72 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3E8K
Number of atoms included #LASTProtein: 12831 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 12831

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