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- PDB-4o4r: Murine Norovirus RdRp in complex with PPNDS -

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Basic information

Entry
Database: PDB / ID: 4o4r
TitleMurine Norovirus RdRp in complex with PPNDS
ComponentsRNA-dependent-RNA-polymerase
KeywordsVIRAL PROTEIN/REPLICATION INHIBITOR / RNA-dependent-RNA-polymerase / RNA binding / VIRAL PROTEIN-REPLICATION 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-20V / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCroci, R. / Tarantino, D. / Milani, M. / Pezzullo, M. / Bolognesi, M. / Mastrangelo, E.
CitationJournal: Febs Lett. / Year: 2014
Title: PPNDS inhibits murine Norovirus RNA-dependent RNA-polymerase mimicking two RNA stacking bases.
Authors: Croci, R. / Tarantino, D. / Milani, M. / Pezzullo, M. / Rohayem, J. / Bolognesi, M. / Mastrangelo, E.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)179,90619
Polymers175,3063
Non-polymers4,59916
Water13,475748
1
A: RNA-dependent-RNA-polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2259
Polymers58,4351
Non-polymers1,7898
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-dependent-RNA-polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0337
Polymers58,4351
Non-polymers1,5976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-dependent-RNA-polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6483
Polymers58,4351
Non-polymers1,2132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.710, 197.430, 109.570
Angle α, β, γ (deg.)90.00, 114.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 58435.422 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1181-1687
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-20V / 3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid / PPNDS / Pyridoxal-5'-phosphate-6-(2'-naphthylazo-6'-nitro-4',8'-disulfonic acid)


Mass: 606.434 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H15N4O14PS2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 293.15 K / Method: macrobatch / pH: 8.4
Details: 1.6M (NH4)2SO4, 12% glycerol, 100mM TRIS/HCl, pH 8.4, macrobatch, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→59.4 Å / Num. obs: 90345 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.53 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PXSOFTdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UQS

3uqs


Resolution: 2.4→59.36 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 4532 5 %RANDOM
Rwork0.19151 ---
all0.19439 ---
obs0.19439 85810 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20.11 Å2
2--0.03 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11355 0 284 748 12387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211940
X-RAY DIFFRACTIONr_bond_other_d00.0211124
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.99616233
X-RAY DIFFRACTIONr_angle_other_deg3.5263.00125635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99851426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92423.103535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.203152001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.08815107
X-RAY DIFFRACTIONr_chiral_restr0.0740.21708
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113301
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022692
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 355 -
Rwork0.321 6253 -
obs--99.98 %

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