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- PDB-3sfu: crystal structure of murine norovirus RNA dependent RNA polymeras... -

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Basic information

Entry
Database: PDB / ID: 3sfu
Titlecrystal structure of murine norovirus RNA dependent RNA polymerase in complex with ribavirin
ComponentsRNA polymerase
KeywordsTRANSFERASE / Right handed fold / VIRAL REPLICATION ENZYME / RNA binding
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Helix non-globular / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-RBV / Genome polyprotein
Similarity search - Component
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsKim, K.H. / Alam, I.
CitationJournal: Virology / Year: 2012
Title: Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase in complex with 2-thiouridine or ribavirin.
Authors: Alam, I. / Lee, J.H. / Cho, K.J. / Han, K.R. / Yang, J.M. / Chung, M.S. / Kim, K.H.
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 9, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase
B: RNA polymerase
C: RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,35262
Polymers175,5593
Non-polymers5,79459
Water8,701483
1
A: RNA polymerase
hetero molecules

A: RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,95542
Polymers117,0392
Non-polymers3,91640
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
2
B: RNA polymerase
C: RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,87541
Polymers117,0392
Non-polymers3,83639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.952, 196.084, 109.206
Angle α, β, γ (deg.)90.00, 114.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein RNA polymerase


Mass: 58519.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Gene: RdRp / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q80J95

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Non-polymers , 5 types, 542 molecules

#2: Chemical ChemComp-RBV / 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide / Ribavirin


Mass: 244.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H12N4O5 / Comment: medication, antivirus*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.26M ammonium sulphate, CHES (pH 9.5), 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 78946 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.093 / Rsym value: 0.461 / Net I/σ(I): 21.41

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.501→47.848 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.81 / σ(F): 1.33 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 2000 2.53 %
Rwork0.1811 --
obs0.1824 78903 99.63 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.602 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 215.1 Å2 / Biso min: 3.32 Å2
Baniso -1Baniso -2Baniso -3
1-10.268 Å20 Å20.0998 Å2
2---1.7162 Å20 Å2
3----8.5518 Å2
Refinement stepCycle: LAST / Resolution: 2.501→47.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11484 0 345 483 12312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812128
X-RAY DIFFRACTIONf_angle_d1.14116405
X-RAY DIFFRACTIONf_dihedral_angle_d17.0254626
X-RAY DIFFRACTIONf_chiral_restr0.0771709
X-RAY DIFFRACTIONf_plane_restr0.0052094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.501-2.56350.32511370.2454525496
2.5635-2.63280.28611420.22275440100
2.6328-2.71030.2631420.2045521100
2.7103-2.79770.26051440.20845509100
2.7977-2.89770.3191420.20725479100
2.8977-3.01370.29061440.21045511100
3.0137-3.15090.26931430.19815509100
3.1509-3.31690.25671430.18655495100
3.3169-3.52470.21361430.17975535100
3.5247-3.79670.17781440.16835509100
3.7967-4.17860.2131430.14625504100
4.1786-4.78280.1721450.14725540100
4.7828-6.02390.22971430.17515533100
6.0239-47.85650.19271450.18025564100

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