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- PDB-2xyz: De Novo model of Bacteriophage P22 virion coat protein -

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Basic information

Entry
Database: PDB / ID: 2xyz
TitleDe Novo model of Bacteriophage P22 virion coat protein
ComponentsCOAT PROTEIN
KeywordsVIRUS / MATURATION / DSDNA VIRUS
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral procapsid maturation / viral procapsid / T=7 icosahedral viral capsid / viral capsid / protein homodimerization activity / identical protein binding / Major capsid protein / Major capsid protein
Function and homology information
Specimen sourceENTEROBACTERIA PHAGE P22 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G
AuthorsChen, D.-H. / Baker, M.L. / Hryc, C.F. / DiMaio, F. / Jakana, J. / Wu, W. / Dougherty, M. / Haase-Pettingell, C. / Schmid, M.F. / Jiang, W. / Baker, D. / King, J.A. / Chiu, W.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.
Authors: Dong-Hua Chen / Matthew L Baker / Corey F Hryc / Frank DiMaio / Joanita Jakana / Weimin Wu / Matthew Dougherty / Cameron Haase-Pettingell / Michael F Schmid / Wen Jiang / David Baker / Jonathan A King / Wah Chiu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 19, 2010 / Release: Feb 2, 2011
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 2, 2011Structure modelrepositoryInitial release
1.1Oct 3, 2018Structure modelData collectiondiffrn_radiation / diffrn_radiation_wavelength / em_software_em_software.image_processing_id

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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
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1826
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  • Superimposition on EM map
  • EMDB-1826
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)327,5697
Polyers327,5697
Non-polymers00
Water0
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)19,654,157420
Polyers19,654,157420
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: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
x 5


  • icosahedral pentamer
  • 1.64 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,637,84635
Polyers1,637,84635
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
x 6


  • icosahedral 23 hexamer
  • 1.97 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,965,41642
Polyers1,965,41642
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
COAT PROTEIN / P22 / PROTEIN GP5 / Coordinate model: Cα atoms only


Mass: 46795.613 Da / Num. of mol.: 7 / Source: (natural) ENTEROBACTERIA PHAGE P22 (bacteriophage) / References: UniProt: A8CGC7, UniProt: P26747*PLUS

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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: BACTERIOPHAGE P22 VIRION / Type: VIRUS / Details: BAD MICROGRAPHS WERE EXCLUDED VISUALLY
Buffer solutionName: 50 MM TRIS PH 7.6, 25 MM NACL / Details: 50 MM TRIS PH 7.6, 25 MM NACL / pH: 7.6
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 4.2, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL KYOTO-3000SFF / Date: Dec 6, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 / Calibrated magnification: 60000 / Nominal defocus max: 2300 nm / Nominal defocus min: 300 nm / Cs: 1.6 mm
Specimen holderTemperature: 4.2 kelvins
Image recordingElectron dose: 36 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 1262

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Processing

EM softwareName: EMAN / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: I
3D reconstructionMethod: FOURIER METHODS / Resolution: 4 Å / Number of particles: 18300 / Nominal pixel size: 1.06 / Actual pixel size: 1.06
Details: MAKE3D IN EMAN. C-TERMINAL 5 RESIDUES WERE NOT MODELE MODELED SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1826.
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--EM / Ref protocol: OTHER / Ref space: REAL / Target criteria: FSC
Least-squares processHighest resolution: 4 Å
Refine hist #LASTHighest resolution: 4 Å
Number of atoms included #LASTProtein: 2975 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2975

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