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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
DescriptorCOAT PROTEIN
KeywordsVIRUS / MATURATION / DSDNA VIRUS
Specimen sourceENTEROBACTERIA PHAGE P22 / virus
MethodElectron microscopy (4 A resolution / Single particle / Vitreous ice)
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.
CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 1355-1360

Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 1355-1360 StrPapers
Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.
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

DateDeposition: Nov 19, 2010 / Release: Feb 2, 2011 / Last modification: Feb 9, 2011

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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
  • EMDB-1826
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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)327,5737
Polyers327,5737
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)19,654,376420
Polyers19,654,376420
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)1,637,86535
Polyers1,637,86535
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)1,965,43842
Polyers1,965,43842
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)
COAT PROTEIN / P22 / PROTEIN GP5


Mass: 46796.133 Da / Num. of mol.: 7 / Source: (natural) ENTEROBACTERIA PHAGE P22 / virus / References: UniProt: A8CGC7

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

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Sample preparation

Assembly of specimenName: BACTERIOPHAGE P22 VIRION / Aggregation state: PARTICLE / Details: BAD MICROGRAPHS WERE EXCLUDED VISUALLY
Buffer solutionName: 50 MM TRIS PH 7.6, 25 MM NACL
Sample preparationpH: 7.6 / Sample conc.: 1 mg/ml
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: 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 / Electron dose: 36 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Calibrated magnification: 60000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 300 nm / Cs: 1.6 mm
Specimen holderTemperature: 4.2 K
CameraType: KODAK SO163 FILM
EM image scansNumber digital images: 1262
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: EMAN / Number of particles: 18300
3D reconstructionMethod: FOURIER METHODS / Resolution: 4 A / Nominal pixel size: 1.06 A/pix / Actual pixel size: 1.06 A/pix / CTF correction method: EACH PARTICLE
Details: MAKE3D IN EMAN. C-TERMINAL 5 RESIDUES WERE NOT MODELE MODELED SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1826.
Atomic model buildingRef protocol: EM / Ref space: REAL / Target criteria: FSC
Least-squares processHighest resolution: 4 A
Refine hist #LASTHighest resolution: 4 A
Number of atoms included #LASTProtein: 2975 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2975

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