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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
Components
  • NUCLEOPROTEIN
  • POLY-URIDINE
KeywordsVIRUS / RNA / NSRV / HELIX / VIRION / VIRAL NUCLEOPROTEIN
Function / homology
Function and homology information


RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesVESICULAR STOMATITIS INDIANA VIRUS
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.6 Å
AuthorsGe, P. / Tsao, J. / Green, T.J. / Luo, M. / Zhou, Z.H.
CitationJournal: Science / Year: 2010
Title: Cryo-EM model of the bullet-shaped vesicular stomatitis virus.
Authors: Peng Ge / Jun Tsao / Stan Schein / Todd J Green / Ming Luo / Z Hong Zhou /
Abstract: Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo-electron microscopy, we show that each ...Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo-electron microscopy, we show that each virion contains two nested, left-handed helices: an outer helix of matrix protein M and an inner helix of nucleoprotein N and RNA. M has a hub domain with four contact sites that link to neighboring M and N subunits, providing rigidity by clamping adjacent turns of the nucleocapsid. Side-by-side interactions between neighboring N subunits are critical for the nucleocapsid to form a bullet shape, and structure-based mutagenesis results support this description. Together, our data suggest a mechanism of VSV assembly in which the nucleocapsid spirals from the tip to become the helical trunk, both subsequently framed and rigidified by the M layer.
History
DepositionNov 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Derived calculations / Other / Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description ...Data collection / Refinement description / Source and taxonomy / Structure summary
Category: em_3d_fitting / em_software ...em_3d_fitting / em_software / entity / entity_src_nat
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _entity.src_method
Revision 1.3Oct 23, 2019Group: Data collection / Derived calculations / Other / Category: cell / struct_conn / Item: _cell.Z_PDB / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _refine.ls_d_res_high

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Structure visualization

Movie
  • Biological unit as representative helical assembly
  • Imaged by Jmol
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  • Deposited structure unit
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Structure viewerMolecule:
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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
Polymers502,10412
Non-polymers00
Water00
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
Polymers7,531,567180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation14
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 15 / Rise per n subunits: 6.981 Å / Rotation per n subunits: -48 °)
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (0.669131, -0.743145), (0.743145, 0.669131), (1) / Vector: -6.98065)

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Components

#1: Protein
NUCLEOPROTEIN / NUCLEOCAPSID PROTEIN / NP / PROTEIN N


Mass: 47463.949 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) VESICULAR STOMATITIS INDIANA VIRUS / Strain: SAN JUAN / References: UniProt: P03521
#2: RNA chain POLY-URIDINE


Mass: 13732.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) VESICULAR STOMATITIS INDIANA VIRUS / Strain: SAN JUAN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: VSV (INDIANA) / Type: VIRUS
Buffer solutionName: 100MM NACL, 10NM TRIS, 1MM EDTA / pH: 7.4 / Details: 100MM NACL, 10NM TRIS, 1MM EDTA
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
MicroscopyModel: 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 X / Calibrated magnification: 98000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderTemperature: 80 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS
Image scansNum. digital images: 212
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2EMAN3D reconstruction
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 10.6 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1663.
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY REFINEMENT
Atomic model buildingPDB-ID: 2WYY

Accession code: 2WYY / Source name: PDB / Type: experimental model
RefinementHighest resolution: 10.6 Å
Refinement stepCycle: LAST / Highest resolution: 10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32820 1800 0 0 34620

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