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- PDB-9evw: Avian reovirus nonstructural protein sigmaNS -

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Basic information

Entry
Database: PDB / ID: 9evw
TitleAvian reovirus nonstructural protein sigmaNS
ComponentsSigma NS
KeywordsVIRAL PROTEIN / Avian orthoreovirus / Nonstructural protein / RNA chaperone / Viroplasm
Function / homologyReovirus non-structural protein sigma NS / Sigma NS protein / single-stranded RNA binding / RNA-directed RNA polymerase activity / Sigma NS
Function and homology information
Biological speciesAvian orthoreovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKascakova, B. / Tuma, R.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000441European Union
Czech Science Foundation22-25396S Czech Republic
Citation
Journal: To Be Published
Title: RNA chaperone activity of reovirus sigmaNS is coupled to ribonucleoprotein filament assembly
Authors: Bravo, J.P.K. / Aspinall, L. / Kascakova, B. / Bartnik, K. / Thompson, R.F. / Lamb, D.C. / Tuma, R. / Borodavka, A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionApr 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sigma NS
B: Sigma NS
C: Sigma NS
D: Sigma NS
E: Sigma NS
F: Sigma NS
G: Sigma NS
H: Sigma NS


Theoretical massNumber of molelcules
Total (without water)323,9528
Polymers323,9528
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Sigma NS / Sigma-NS protein


Mass: 40494.004 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian orthoreovirus / Strain: 1733 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DH28
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Octameric non-structural protein sigmaNS from avian reovirus with swapped N-termini
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.32 MDa / Experimental value: YES
Source (natural)Organism: Avian orthoreovirus
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusIsolate: OTHER
Buffer solutionpH: 7.6 / Details: 20 mM Tris, 100 mM NaCl, 0.5 mM MgCl2
SpecimenConc.: 0.386 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80.4 K / Temperature (min): 80.4 K
Image recordingAverage exposure time: 3.37 sec. / Electron dose: 45 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 15847
Details: First grid: 6945 movies at 0 degrees tilt, 1720 movies at 30 degrees tilt Second grid: 7182 movies at 30 degrees tilt
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1crYOLO1.6.1particle selection
2EPU3.2image acquisition
4CTFFIND4.1.14CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1601697
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236226 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 127.43 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003322830
ELECTRON MICROSCOPYf_angle_d0.661730919
ELECTRON MICROSCOPYf_chiral_restr0.03853465
ELECTRON MICROSCOPYf_plane_restr0.00474088
ELECTRON MICROSCOPYf_dihedral_angle_d4.94243189

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