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- PDB-8tl8: Structure of Orthoreovirus RNA Chaperone SigmaNS R6A mutant in co... -

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Basic information

Entry
Database: PDB / ID: 8tl8
TitleStructure of Orthoreovirus RNA Chaperone SigmaNS R6A mutant in complex with bile acid
ComponentsProtein sigma-NS
KeywordsRNA BINDING PROTEIN / RNA-binding protein / RNA chaperone
Function / homologyReovirus non-structural protein sigma NS / Sigma NS protein / host cell cytoplasm / single-stranded RNA binding / RNA-directed RNA polymerase activity / GLYCOCHOLIC ACID / Protein sigma-NS
Function and homology information
Biological speciesOrthoreovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPrasad, B.V.V. / Zhao, B. / Hu, L. / Neetu, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentR01 AI032539 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure of orthoreovirus RNA chaperone sigma NS, a component of viral replication factories.
Authors: Zhao, B. / Hu, L. / Kaundal, S. / Neetu, N. / Lee, C.H. / Somoulay, X. / Sankaran, B. / Taylor, G.M. / Dermody, T.S. / Venkataram Prasad, B.V.
History
DepositionJul 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein sigma-NS
B: Protein sigma-NS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0726
Polymers82,2092
Non-polymers1,8624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-1 kcal/mol
Surface area29630 Å2
Unit cell
Length a, b, c (Å)54.129, 54.129, 305.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Protein sigma-NS / SigmaNS


Mass: 41104.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthoreovirus / Gene: S3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03526
#2: Chemical
ChemComp-GCH / GLYCOCHOLIC ACID / N-CHOLYLGLYCINE


Mass: 465.623 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H43NO6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.2% colic acid derivative mix, 0.1 M Buffer System 3 (pH 8.5), and 30% Precipitant Mix 3 (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→76.38 Å / Num. obs: 12953 / % possible obs: 81.7 % / Redundancy: 1 % / Biso Wilson estimate: 62.51 Å2 / Rmerge(I) obs: 0.0311 / Rpim(I) all: 0.0311 / Rrim(I) all: 0.04398 / Net I/σ(I): 18.04
Reflection shell
Resolution (Å)Num. unique obsCC1/2CC starRpim(I) allRrim(I) allDiffraction-ID
3.1-3.158500.6390.8830.4091.2421
3.15-3.219400.6840.3461.031

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→34.22 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 639 5.43 %RANDOM
Rwork0.2203 ---
obs0.2216 11775 81.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→34.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 132 0 5337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035457
X-RAY DIFFRACTIONf_angle_d0.5847408
X-RAY DIFFRACTIONf_dihedral_angle_d5.25842
X-RAY DIFFRACTIONf_chiral_restr0.043888
X-RAY DIFFRACTIONf_plane_restr0.005921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.31791290.28472186X-RAY DIFFRACTION82
3.45-3.80.33081200.25422206X-RAY DIFFRACTION81
3.8-4.340.24761250.22362223X-RAY DIFFRACTION82
4.35-5.470.21781330.20762207X-RAY DIFFRACTION81
5.47-34.220.19361320.18612314X-RAY DIFFRACTION85

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