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- PDB-2wyy: CRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS -

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Basic information

Entry
Database: PDB / ID: 2wyy
TitleCRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS
DescriptorNUCLEOPROTEIN
KeywordsVIRUS / RNA / NSRV / HELIX / VIRION / VIRAL NUCLEOPROTEIN
Specimen sourceVESICULAR STOMATITIS INDIANA VIRUS / virus / VSV
MethodElectron microscopy (10.6 A resolution / Helical / Vitreous ice (cryo EM))
AuthorsGe, P. / Tsao, J. / Green, T.J. / Luo, M. / Zhou, Z.H.
CitationScience, 2010, 327, 689-693

Science, 2010, 327, 689-693 StrPapers
Cryo-EM model of the bullet-shaped vesicular stomatitis virus.
Peng Ge / Jun Tsao / Stan Schein / Todd J Green / Ming Luo / Z Hong Zhou

DateDeposition: Nov 20, 2009 / Release: Feb 16, 2010 / Last modification: Aug 24, 2011

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Structure visualization

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Assembly

Deposited unit
A: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
F: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: NUCLEOPROTEIN
J: NUCLEOPROTEIN
K: NUCLEOPROTEIN
L: NUCLEOPROTEIN
M: NUCLEOPROTEIN
R: POLY-URIDINE
S: POLY-URIDINE


Theoretical massNumber of molelcules
Total (without water)502,10912
Polyers502,10912
Non-polymers00
Water0
#1
A: NUCLEOPROTEIN
C: NUCLEOPROTEIN
D: NUCLEOPROTEIN
F: NUCLEOPROTEIN
H: NUCLEOPROTEIN
I: NUCLEOPROTEIN
J: NUCLEOPROTEIN
K: NUCLEOPROTEIN
L: NUCLEOPROTEIN
M: NUCLEOPROTEIN
R: POLY-URIDINE
S: POLY-URIDINE
x 15


Theoretical massNumber of molelcules
Total (without water)7,531,639180
Polyers7,531,639180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation15
#2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
HAU


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1

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Components

#1: Polypeptide(L)
NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / NP / PROTEIN N


Mass: 47464.406 Da / Num. of mol.: 10
Source: (natural) VESICULAR STOMATITIS INDIANA VIRUS / virus
References: UniProt: P03521

Cellular component

Molecular function

Biological process

#2: RNA chainPOLY-URIDINE


Mass: 13732.619 Da / Num. of mol.: 2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimen
IDNameAggregation stateDetails
1VSV (INDIANA)FILAMENT
2DATA AQUISITION
Buffer solutionName: 100MM NACL, 10NM TRIS, 1MM EDTA
Sample preparationpH: 7.4
VitrificationDetails: CRYOGEN - ETHANE, HUMIDITY - 50, TEMPERATURE - 80, INSTRUMENT - MANUAL PLUNGER, METHOD- MANUAL BLOT 1 SECOND BEFORE PLUNGING, DETAILS - VITRIFICATION CARRIED OUT IN OPEN ROOM.

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Electron microscopy imaging

MicroscopyDate: Jan 5, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: SPOT SCAN
Electron lensNominal magnification: 59000 X / Calibrated magnification: 98000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderTemperature: 80 K
CameraType: TIETZ CCD
EM image scansNumber digital images: 212
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: EMAN
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 10.6 A
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1663.
Atomic model buildingMethod: RIGID BODY / Ref protocol: RIGID BODY REFINEMENT / Ref space: REAL / Target criteria: CROSS-CORRELATION
Atomic model buildingPDB-ID: 2WYY
Least-squares processHighest resolution: 1 A
Refine hist #LASTHighest resolution: 1 A
Number of atoms included #LASTProtein: 32820 / Nucleic acid: 1800 / Ligand: 0 / Solvent: 0 / Total: 34620

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