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- PDB-8tka: Structure of Orthoreovirus RNA Chaperone SigmaNS R6A mutant -

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Basic information

Entry
Database: PDB / ID: 8tka
TitleStructure of Orthoreovirus RNA Chaperone SigmaNS R6A mutant
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 / Protein sigma-NS
Function and homology information
Biological speciesMammalian orthoreovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 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 25, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)84,2732
Polymers84,2732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-8 kcal/mol
Surface area33420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.111, 137.111, 98.248
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Protein sigma-NS / SigmaNS


Mass: 42136.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 1 / Gene: S3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03526
Has ligand of interestY
Has protein modificationY

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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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2% colic acid derivative, 0.1M buffer system 3 and 30% precipitant mix 3 (molecular dimension)

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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: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→118.74 Å / Num. obs: 41323 / % possible obs: 99.64 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 8.5
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.069 / Num. unique obs: 29506 / Rpim(I) all: 0.023

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 3→118.74 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.881 / SU B: 24.392 / SU ML: 0.426 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28855 1085 5.1 %RANDOM
Rwork0.23061 ---
obs0.23349 20041 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.303 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å2-0 Å2
3----3.5 Å2
Refinement stepCycle: 1 / Resolution: 3→118.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 0 0 5494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195580
X-RAY DIFFRACTIONr_bond_other_d0.0030.025308
X-RAY DIFFRACTIONr_angle_refined_deg1.5792.0037538
X-RAY DIFFRACTIONr_angle_other_deg1.074312269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75522.926229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20715890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3491552
X-RAY DIFFRACTIONr_chiral_restr0.0780.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216118
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021122
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_it5.3167.8272828
X-RAY DIFFRACTIONr_mcbond_other5.317.8282827
X-RAY DIFFRACTIONr_mcangle_it8.57711.7643528
X-RAY DIFFRACTIONr_mcangle_other8.57811.7633529
X-RAY DIFFRACTIONr_scbond_it5.4498.3112752
X-RAY DIFFRACTIONr_scbond_other5.4488.3112753
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.76912.2654011
X-RAY DIFFRACTIONr_long_range_B_refined12.67295.3126101
X-RAY DIFFRACTIONr_long_range_B_other12.67195.3146102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 85 -
Rwork0.302 1479 -
obs--99.62 %

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