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- PDB-5i61: Crystal structure of the RNA-dependent RNA polymerase of a human ... -

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Basic information

Entry
Database: PDB / ID: 5i61
TitleCrystal structure of the RNA-dependent RNA polymerase of a human picorbirnavirus
ComponentsPotential RNA-dependent RNA polymerase
Keywordsviral protein / transcription / dsRNA / replication / insertion loop
Function / homology
Function and homology information


virion component / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Potential RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesHuman picobirnavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsCollier, A.M. / Guo, Y.R. / Tao, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AIO67638 United States
CitationJournal: Plos Pathog. / Year: 2016
Title: Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus.
Authors: Collier, A.M. / Lyytinen, O.L. / Guo, Y.R. / Toh, Y. / Poranen, M.M. / Tao, Y.J.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references / Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Potential RNA-dependent RNA polymerase
A: Potential RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)123,8312
Polymers123,8312
Non-polymers00
Water5,170287
1
A: Potential RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)61,9151
Polymers61,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Potential RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)61,9151
Polymers61,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.756, 78.763, 101.449
Angle α, β, γ (deg.)90.000, 91.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Potential RNA-dependent RNA polymerase


Mass: 61915.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human picobirnavirus (strain Human/Thailand/Hy005102/-)
Strain: Human/Thailand/Hy005102/- / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q50LE4, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM sodium acetate, 100 mM sodium cacodylate pH 6.5, and 30% PEG 8000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9785 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Nov 21, 2011
RadiationMonochromator: Rosenbaum-Rock Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 44254 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.067 / Rrim(I) all: 0.132 / Χ2: 1.777 / Net I/av σ(I): 13.364 / Net I/σ(I): 7.7 / Num. measured all: 165286
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.27-2.312.70.48120060.6820.3420.5930.45890.4
2.31-2.353.10.4721380.7260.310.5660.48896.4
2.35-2.43.70.43922120.8070.2660.5140.40499.7
2.4-2.453.80.38821980.8460.2320.4530.415100
2.45-2.53.80.35622130.8660.2120.4150.46100
2.5-2.563.80.33322370.8870.1980.3880.47899.9
2.56-2.623.80.29922100.8990.1780.3480.589100
2.62-2.693.80.27322070.9160.1620.3180.667100
2.69-2.773.80.24422290.930.1450.2840.726100
2.77-2.863.90.22221980.9420.1310.2580.869100
2.86-2.963.90.19422130.9410.1150.2261.051100
2.96-3.083.80.17522390.9560.1030.2031.27199.9
3.08-3.223.90.14922310.9690.0890.1741.49100
3.22-3.393.80.13322170.9720.0790.1551.98499.9
3.39-3.63.90.11322250.9770.0670.1322.41799.9
3.6-3.883.90.09522250.9840.0570.1112.62199.9
3.88-4.273.80.07622420.9910.0450.0892.89100
4.27-4.893.80.05922400.9950.0350.0692.699100
4.89-6.163.80.07122650.9920.0410.0823.6100
6.16-503.70.06623090.9960.0390.0778.717100

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.795 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1923 5.11 %
Rwork0.1698 35681 -
obs0.1725 37604 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.81 Å2 / Biso mean: 38.3836 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 2.4→43.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8284 0 0 287 8571
Biso mean---35.3 -
Num. residues----1033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018490
X-RAY DIFFRACTIONf_angle_d1.0811494
X-RAY DIFFRACTIONf_chiral_restr0.0551220
X-RAY DIFFRACTIONf_plane_restr0.0071472
X-RAY DIFFRACTIONf_dihedral_angle_d14.4235063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.460.26811290.192725632692
2.46-2.52660.26071270.194325562683
2.5266-2.60090.28731260.198925182644
2.6009-2.68480.2821480.199725262674
2.6848-2.78080.2731300.20225452675
2.7808-2.89210.2691490.191825222671
2.8921-3.02370.25181550.182125242679
3.0237-3.18310.2471360.177225392675
3.1831-3.38240.20981720.171125092681
3.3824-3.64350.21411550.158725072662
3.6435-4.00990.18981200.147525832703
4.0099-4.58960.17551270.136425652692
4.5896-5.78030.21531000.162925962696
5.7803-43.80260.20881490.182226282777

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