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

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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 Å resolution / Filament / Helical)
AuthorsGe, P. / Tsao, J. / Green, T.J. / Luo, M. / Zhou, Z.H.
CitationScience, 2010, 327, 689-693

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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2009 / Release: Feb 16, 2010
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 16, 2010Structure modelrepositoryInitial release
1.1Aug 24, 2011Structure modelDerived calculations / Other / Version format compliance
1.2Aug 23, 2017Structure modelData collection / Refinement description / Source and taxonomy / Structure summaryem_3d_fitting / em_software / entity / entity_src_nat_em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _entity.src_method

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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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)502,10412
Polyers502,10412
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)7,531,567180
Polyers7,531,567180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation15
#2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
#3


  • 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: 47463.949 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: 13732.498 Da / Num. of mol.: 2
Source: (natural) VESICULAR STOMATITIS INDIANA VIRUS / virus

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

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Sample preparation

ComponentName: VSV (INDIANA) / Type: VIRUS
Buffer solutionName: 100MM NACL, 10NM TRIS, 1MM EDTA / Details: 100MM NACL, 10NM TRIS, 1MM EDTA / pH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: 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

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300 / Date: Jan 5, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 / Calibrated magnification: 98000 / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderTemperature: 80 kelvins
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS
Image scansNumber digital images: 212
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1UCSF ChimeraMODEL FITTING1
2EMANRECONSTRUCTION1
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 10.6 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1663.
Symmetry type: HELICAL
Atomic model buildingDetails: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY REFINEMENT
Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 2WYY
Least-squares processHighest resolution: 1 Å
Refine hist #LASTHighest resolution: 1 Å
Number of atoms included #LASTProtein: 32820 / Nucleic acid: 1800 / Ligand: 0 / Solvent: 0 / Total: 34620

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