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- PDB-2xd8: Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7 -

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Basic information

Entry
Database: PDB / ID: 2xd8
TitleCapsid structure of the infectious Prochlorococcus Cyanophage P-SSP7
DescriptorT7-LIKE CAPSID PROTEIN
KeywordsVIRUS / MARINE PODOVIRUS / T7-LIKE VIRUS
Specimen sourcePROCHLOROCOCCUS PHAGE P-SSP7 / virus
MethodElectron microscopy (4.6 Å resolution / Particle / Single particle)
AuthorsLiu, X. / Zhang, Q. / Murata, K. / Baker, M.L. / Sullivan, M.B. / Fu, C. / Dougherty, M. / Schmid, M.F. / Osburne, M.S. / Chisholm, S.W. / Chiu, W.
CitationNat. Struct. Mol. Biol., 2010, 17, 830-836

Nat. Struct. Mol. Biol., 2010, 17, 830-836 StrPapers
Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus.
Xiangan Liu / Qinfen Zhang / Kazuyoshi Murata / Matthew L Baker / Matthew B Sullivan / Caroline Fu / Matthew T Dougherty / Michael F Schmid / Marcia S Osburne / Sallie W Chisholm / Wah Chiu

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 30, 2010 / Release: Jun 16, 2010
RevisionDateData content typeGroupProviderType
1.0Jun 16, 2010Structure modelrepositoryInitial release
1.1Mar 20, 2013Structure modelOther / Refinement description / Version 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
  • EMDB-1713
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Assembly

Deposited unit
A: T7-LIKE CAPSID PROTEIN
B: T7-LIKE CAPSID PROTEIN
C: T7-LIKE CAPSID PROTEIN
D: T7-LIKE CAPSID PROTEIN
E: T7-LIKE CAPSID PROTEIN
F: T7-LIKE CAPSID PROTEIN
G: T7-LIKE CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)276,4597
Polyers276,4597
Non-polymers00
Water0
#1
A: T7-LIKE CAPSID PROTEIN
B: T7-LIKE CAPSID PROTEIN
C: T7-LIKE CAPSID PROTEIN
D: T7-LIKE CAPSID PROTEIN
E: T7-LIKE CAPSID PROTEIN
F: T7-LIKE CAPSID PROTEIN
G: T7-LIKE CAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)16,587,569420
Polyers16,587,569420
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: T7-LIKE CAPSID PROTEIN
B: T7-LIKE CAPSID PROTEIN
C: T7-LIKE CAPSID PROTEIN
D: T7-LIKE CAPSID PROTEIN
E: T7-LIKE CAPSID PROTEIN
F: T7-LIKE CAPSID PROTEIN
G: T7-LIKE CAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 1.38 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,382,29735
Polyers1,382,29735
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: T7-LIKE CAPSID PROTEIN
B: T7-LIKE CAPSID PROTEIN
C: T7-LIKE CAPSID PROTEIN
D: T7-LIKE CAPSID PROTEIN
E: T7-LIKE CAPSID PROTEIN
F: T7-LIKE CAPSID PROTEIN
G: T7-LIKE CAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 1.66 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,658,75742
Polyers1,658,75742
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)
T7-LIKE CAPSID PROTEIN / GP10 / Coordinate model: Cα atoms only


Mass: 39494.211 Da / Num. of mol.: 7 / Source: (gene. exp.) PROCHLOROCOCCUS PHAGE P-SSP7 / virus / References: UniProt: Q58N30

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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: CYANOPHAGE P-SSP7 / Type: VIRUS
Buffer solutionName: 100 MM TRIS-HCL, 100 MM MGSO4, AND 30 MM NACL / Details: 100 MM TRIS-HCL, 100 MM MGSO4, AND 30 MM NACL / pH: 7.5
SpecimenConc.: 5 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

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC / Date: Aug 31, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 4.1 mm
Specimen holderTemperature: 101 kelvins
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 1059
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: MPSA / Category: RECONSTRUCTION
CTF correctionDetails: INDIVIDUAL MICROGRAPH
SymmetryPoint symmetry: I
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 4.6 Å / Number of particles: 36000 / Nominal pixel size: 1.27 / Actual pixel size: 1.17 / Magnification calibration: 2D CRYSTAL
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1713.
Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting ID
11IJG1
22JES1
Least-squares processHighest resolution: 4.6 Å
Refine hist #LASTHighest resolution: 4.6 Å
Number of atoms included #LASTProtein: 2541 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2541

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