[English] 日本語
Yorodumi
- PDB-2xd8: Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7 -

+
Open data


ID or keywords:

Loading...

no data

-
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 A resolution / Single particle / Vitreous ice)
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

DateDeposition: Apr 30, 2010 / Release: Jun 16, 2010 / Last modification: Mar 20, 2013

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1713
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
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)276,4627
Polyers276,4627
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)16,587,724420
Polyers16,587,724420
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)1,382,31035
Polyers1,382,31035
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)1,658,77242
Polyers1,658,77242
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

-
Components

#1: Polypeptide(L)
T7-LIKE CAPSID PROTEIN / GP10


Mass: 39494.582 Da / Num. of mol.: 7 / Source: (gene. exp.) PROCHLOROCOCCUS PHAGE P-SSP7 / virus / References: UniProt: Q58N30

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE

-
Sample preparation

Assembly of specimenName: CYANOPHAGE P-SSP7 / Aggregation state: PARTICLE
Buffer solutionName: 100 MM TRIS-HCL, 100 MM MGSO4, AND 30 MM NACL
Sample preparationpH: 7.5 / Sample conc.: 5 mg/ml
Specimen supportDetails: HOLEY CARBON

-
Electron microscopy imaging

MicroscopyMicroscope model: OTHER / Date: Aug 31, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: LOW DOSE
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 4.1 mm
Specimen holderTemperature: 101 K
CameraType: KODAK SO163 FILM
EM image scansNumber digital images: 1059
Radiation wavelengthRelative weight: 1

-
Processing

Image selectionSoftware name: MPSA / Number of particles: 36000
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 4.6 A / Nominal pixel size: 1.27 A/pix / Actual pixel size: 1.17 A/pix / Magnification calibration: 2D CRYSTAL / CTF correction method: INDIVIDUAL MICROGRAPH
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1713.
Atomic model buildingPDB-ID: 1IJG, 2JES
Least-squares processHighest resolution: 4.6 A
Refine hist #LASTHighest resolution: 4.6 A
Number of atoms included #LASTProtein: 2541 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2541

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more