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- PDB-4nru: Murine Norovirus RNA-dependent-RNA-polymerase in complex with Com... -

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Basic information

Entry
Database: PDB / ID: 4nru
TitleMurine Norovirus RNA-dependent-RNA-polymerase in complex with Compound 6, a suramin derivative
ComponentsRNA dependent RNA polymeraseRNA-dependent RNA polymerase
KeywordsVIRAL PROTEIN/TRANSCRIPTION INHIBITOR / RNA dependent RNA polymerase / Murine Norovirus / VIRAL PROTEIN-TRANSCRIPTION INHIBITOR complex
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-2NG / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMilani, M. / Croci, R. / Pezzullo, M. / Tarantino, D. / Mastrangelo, E. / Bolognesi, M.
CitationJournal: Plos One / Year: 2014
Title: Structural bases of norovirus RNA dependent RNA polymerase inhibition by novel suramin-related compounds.
Authors: Croci, R. / Pezzullo, M. / Tarantino, D. / Milani, M. / Tsay, S.C. / Sureshbabu, R. / Tsai, Y.J. / Mastrangelo, E. / Rohayem, J. / Bolognesi, M. / Hwu, J.R.
History
DepositionNov 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA dependent RNA polymerase
B: RNA dependent RNA polymerase
C: RNA dependent RNA polymerase
D: RNA dependent RNA polymerase
E: RNA dependent RNA polymerase
F: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,85719
Polymers350,6136
Non-polymers4,24513
Water30,8781714
1
A: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0453
Polymers58,4351
Non-polymers6102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0453
Polymers58,4351
Non-polymers6102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0453
Polymers58,4351
Non-polymers6102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0453
Polymers58,4351
Non-polymers6102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6314
Polymers58,4351
Non-polymers1,1953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0453
Polymers58,4351
Non-polymers6102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
C: RNA dependent RNA polymerase
D: RNA dependent RNA polymerase
hetero molecules

A: RNA dependent RNA polymerase
B: RNA dependent RNA polymerase
E: RNA dependent RNA polymerase
F: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,85719
Polymers350,6136
Non-polymers4,24513
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_645-x+1,y-1/2,-z1
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-54 kcal/mol
Surface area121740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.220, 162.420, 122.960
Angle α, β, γ (deg.)90.00, 97.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RNA dependent RNA polymerase / RNA-dependent RNA polymerase


Mass: 58435.422 Da / Num. of mol.: 6 / Fragment: UNP Residues 1097-1687
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: S4V9Y7, UniProt: Q80J95*PLUS
#2: Chemical
ChemComp-2NG / 4-({4-methyl-3-[(3-nitrobenzoyl)amino]benzoyl}amino)naphthalene-1,5-disulfonic acid


Mass: 585.562 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C25H19N3O10S2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1714 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 8.4
Details: 1.6M (NH4)2SO4, 12% Glycerol, 100mM TrisHCL pH8.4, microbatch, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2013
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→64.96 Å / Num. obs: 188102 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.42 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
EDNAdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→61.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25396 9440 5 %RANDOM
Rwork0.19085 ---
all0.194 178553 --
obs0.194 178553 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.367 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20.68 Å2
2--0.82 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→61.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22787 0 286 1714 24787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01923718
X-RAY DIFFRACTIONr_bond_other_d00.0222336
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.98432181
X-RAY DIFFRACTIONr_angle_other_deg3.5313.00251478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9852867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18823.0721084
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.515154037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.27215220
X-RAY DIFFRACTIONr_chiral_restr0.0740.23380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02126604
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025450
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 633 -
Rwork0.298 13283 -
obs--99.98 %

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