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- PDB-2xvr: Phage T7 empty mature head shell -

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Basic information

Entry
Database: PDB / ID: 2xvr
TitlePhage T7 empty mature head shell
ComponentsMAJOR CAPSID PROTEIN 10A
KeywordsVIRUS / CAPSID MATURATION / MORPHOGENETIC INTERMEDIATE
Function / homologyCapsid Gp10A/Gp10B / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Specimen sourceENTEROBACTERIA PHAGE T7 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 10.8 Å resolution
AuthorsIonel, A. / Velazquez-Muriel, J.A. / Luque, D. / Cuervo, A. / Caston, J.R. / Valpuesta, J.M. / Martin-Benito, J. / Carrascosa, J.L.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Molecular rearrangements involved in the capsid shell maturation of bacteriophage T7.
Authors: Alina Ionel / Javier A Velázquez-Muriel / Daniel Luque / Ana Cuervo / José R Castón / José M Valpuesta / Jaime Martín-Benito / José L Carrascosa
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 28, 2010 / Release: Dec 1, 2010
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 1, 2010Structure modelrepositoryInitial release
1.1Mar 21, 2012Structure modelOther / Version format compliance
1.2Mar 20, 2013Structure modelOther / Refinement description
1.3Aug 30, 2017Structure modelData collectionem_image_scans
1.4Oct 3, 2018Structure modelData collectiondiffrn_radiation / diffrn_radiation_wavelength / em_software_em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1810
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  • Superimposition on EM map
  • EMDB-1810
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
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Assembly

Deposited unit
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
G: MAJOR CAPSID PROTEIN 10A


Theoretical massNumber of molelcules
Total (without water)256,1277
Polyers256,1277
Non-polymers00
Water0
1
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
G: 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
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
G: 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
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
G: 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: Protein/peptide
MAJOR CAPSID PROTEIN 10A / BACTERIOPHAGE T7


Mass: 36589.625 Da / Num. of mol.: 7 / Source: (natural) ENTEROBACTERIA PHAGE T7 (bacteriophage) / References: UniProt: P19726

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PHAGE T7 EMPTY HEAD / Type: VIRUS
Buffer solutionName: 50 MM TRIS-HCL, PH 7.8, 10 MM MGCL2, 0.1 M NACL / Details: 50 MM TRIS-HCL, PH 7.8, 10 MM MGCL2, 0.1 M NACL / pH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: VITRIFICATION 1 -- CRYOGEN- ETHANE,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: Xmipp / Category: 3D reconstruction
SymmetryPoint symmetry: I
3D reconstructionResolution: 10.8 Å / Number of particles: 5100 / Actual pixel size: 1.4
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1810. (DEPOSITION ID: 7638).
Symmetry type: POINT
Atomic model buildingRef space: REAL
Atomic model buildingPDB-ID: 1OHG
Least-squares processHighest resolution: 10.8 Å
Refine hist #LASTHighest resolution: 10.8 Å
Number of atoms included #LASTProtein: 12831 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 12831

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