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- EMDB-50018: Avian reovirus nonstructural protein sigmaNS -

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Basic information

Entry
Database: EMDB / ID: EMD-50018
TitleAvian reovirus nonstructural protein sigmaNS
Map data
Sample
  • Complex: Octameric non-structural protein sigmaNS from avian reovirus with swapped N-termini
    • Protein or peptide: Sigma NS
KeywordsAvian orthoreovirus / Nonstructural protein / RNA chaperone / Viroplasm / VIRAL PROTEIN
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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsTuma R / Aspinall L
Funding supportEuropean Union, Czech Republic, 2 items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000441European Union
Czech Science Foundation22-25396S Czech Republic
CitationJournal: 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, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50018.png

Downloads & links

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Map

FileDownload / File: emd_50018.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 266.4 Å		1.11 Å/pix.
x 240 pix.
= 266.4 Å		1.11 Å/pix.
x 240 pix.
= 266.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00855
Minimum - Maximum-0.014054118 - 0.043442916
Average (Standard dev.)0.00011102096 (±0.0017601807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 266.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50018_msk_1.map
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Half map: #1

Fileemd_50018_half_map_1.map
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Histogram

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Half map: #2

Fileemd_50018_half_map_2.map
Projections & Slices
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Sample components

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Entire : Octameric non-structural protein sigmaNS from avian reovirus with...

EntireName: Octameric non-structural protein sigmaNS from avian reovirus with swapped N-termini
Components
  • Complex: Octameric non-structural protein sigmaNS from avian reovirus with swapped N-termini
    • Protein or peptide: Sigma NS

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Supramolecule #1: Octameric non-structural protein sigmaNS from avian reovirus with...

SupramoleculeName: Octameric non-structural protein sigmaNS from avian reovirus with swapped N-termini
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Avian orthoreovirus
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: Sigma NS

MacromoleculeName: Sigma NS / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Avian orthoreovirus / Strain: 1733
Molecular weightTheoretical: 40.494004 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DNTVRVGVSR NTSGAAGQTL FRNFYLLRCN ILADGRNATK AVQSHFPFLS RAVRCLSPLA AHCADRTLRR DNVKQILTRE LPFSSDLIN YAHHVNSSSL TTSQGVEAAR LVAQVYGEQV PFDHIYPTGS ATYCPGAIAN AISRIMAGFV PREGDDFAPS G PIDYLAAD ...String:
DNTVRVGVSR NTSGAAGQTL FRNFYLLRCN ILADGRNATK AVQSHFPFLS RAVRCLSPLA AHCADRTLRR DNVKQILTRE LPFSSDLIN YAHHVNSSSL TTSQGVEAAR LVAQVYGEQV PFDHIYPTGS ATYCPGAIAN AISRIMAGFV PREGDDFAPS G PIDYLAAD LIAYKFVLPY MLDMVDGRPQ IVLPSHTVEE MLTNTSLLNS IDASFGIEAR SDQRMTRDAA EMSSRSLNEL ED HDQRGRM PWKIMLGMMA AQLKVELDAL ADERTESQAN AHVTSFGSRL FNQMSAFVTI DHELMELALL IKEQGFAMNP GQI ASKWSL IRRSGPTRPL SGARLEIRNG NWMIREGDQT LLSVSPARMA

UniProtKB: Sigma NS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.386 mg/mL
BufferpH: 7.6 / Details: 20 mM Tris, 100 mM NaCl, 0.5 mM MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.4 K / Max: 80.4 K
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 15847 / Average exposure time: 3.37 sec. / Average electron dose: 45.0 e/Å2
Details: First grid: 6945 movies at 0 degrees tilt, 1720 movies at 30 degrees tilt Second grid: 7182 movies at 30 degrees tilt
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1601697
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 236226
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 49436 / Software - Name: RELION (ver. 4.0)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9evw:
Avian reovirus nonstructural protein sigmaNS

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