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- PDB-8tl1: Structure of Orthoreovirus RNA Chaperone SigmaNS N17 -

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Basic information

Entry
Database: PDB / ID: 8tl1
TitleStructure of Orthoreovirus RNA Chaperone SigmaNS N17
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-dependent RNA polymerase activity / GLYCOCHOLIC ACID / Protein sigma-NS
Function and homology information
Biological speciesOrthoreovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsPrasad, B.V.V. / Zhao, B. / Hu, L.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1893
Polymers39,2571
Non-polymers9312
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint1 kcal/mol
Surface area15870 Å2
Unit cell
Length a, b, c (Å)77.522, 76.801, 89.090
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein sigma-NS / SigmaNS


Mass: 39257.469 Da / Num. of mol.: 1
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 / Glycocholic acid


Mass: 465.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H43NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2% colic acid derivativemix, 0.1 M buffer system 3 (8.5), 30% precipitant Mix3 (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: 3.16→88.84 Å / Num. obs: 7841 / % possible obs: 86.39 % / Redundancy: 1 % / Rmerge(I) obs: 0.1319 / Net I/σ(I): 10.09
Reflection shellResolution: 3.2→3.2 Å / Rmerge(I) obs: 0.13 / Num. unique obs: 302 / Rpim(I) all: 0.13 / Rsym value: 0.18

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.16→88.84 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 24.65 / SU ML: 0.406 / Cross valid method: THROUGHOUT / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 457 5.8 %RANDOM
Rwork0.20818 ---
obs0.21096 7380 86.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.755 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.42 Å2
2--0.56 Å20 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 3.16→88.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 66 5 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192752
X-RAY DIFFRACTIONr_bond_other_d0.0020.022621
X-RAY DIFFRACTIONr_angle_refined_deg1.462.013732
X-RAY DIFFRACTIONr_angle_other_deg0.95436080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3375334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15123.07114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.13215494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8251525
X-RAY DIFFRACTIONr_chiral_restr0.0720.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212952
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02544
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.163→3.245 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 18 -
Rwork0.29 203 -
obs--32.64 %

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