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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 A resolution / Single particle / Vitreous ice (cryo EM))
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 StrPapers
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 StrPapers
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.

DateDeposition: Oct 27, 2010 / Release: Nov 17, 2010 / Last modification: Feb 9, 2011

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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
  • EMDB-1321
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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)256,1297
Polyers256,1297
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)15,367,761420
Polyers15,367,761420
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)1,280,64735
Polyers1,280,64735
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)1,536,77642
Polyers1,536,77642
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 capsid protein 10A


Mass: 36589.906 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: bacteriophage T7 prohead / Aggregation state: PARTICLE
ComponentName: gp10A
Details of the virusVirus host category: Bacteria / Virus host growth cell: Escherichia coli / Virus host species: Escherichia coli / Virus type: Prohead virion
Buffer solutionName: 50mM Tris-HCl pH:7.7 10mM MgCl2 100mM NaCl
Sample preparationpH: 7.7
Specimen supportDetails: Quantifoil R2/2 carbon grids
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: Tecnai G2
Electron gunElectron source: Field Emission Gun / Accelerating voltage: 200 kV / Electron dose: 10 e/A2 / Illumination mode: SPOT SCAN
Electron lensMode: Bright field / Nominal magnification: 50000 X / Calibrated magnification: 51600 X / 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.
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

EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: Spider / Software: Spider / Resolution: 10.9 A / Actual pixel size: 2.72 A/pix / CTF correction method: Wiener filter, defocus groups
Atomic model buildingPDB-ID: 3IZG
Number of atoms included #LASTProtein: 12831 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 12831

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