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- PDB-3uqs: Crystal structures of murine norovirus RNA-dependent RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 3uqs
TitleCrystal structures of murine norovirus RNA-dependent RNA polymerase
ComponentsRNA-dependent RNA polymerase
KeywordsTRANSFERASE / RNA-dependent RNA polymerase
Function / homology
Function and homology information


calicivirin / 5'-3' RNA polymerase activity / host cell mitochondrion / host cell endosome membrane / nucleoside-triphosphate phosphatase / ribonucleoside triphosphate phosphatase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity ...calicivirin / 5'-3' RNA polymerase activity / host cell mitochondrion / host cell endosome membrane / nucleoside-triphosphate phosphatase / ribonucleoside triphosphate phosphatase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / metal ion binding / extracellular region / ATP 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 / Helix non-globular / Special / 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 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / 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
Biological speciesmurine norovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMilani, M. / Mastrangelo, E. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structure-Based Inhibition of Norovirus RNA-Dependent RNA Polymerases.
Authors: Mastrangelo, E. / Pezzullo, M. / Tarantino, D. / Petazzi, R. / Germani, F. / Kramer, D. / Robel, I. / Rohayem, J. / Bolognesi, M. / Milani, M.
History
DepositionNov 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)176,55516
Polymers175,3063
Non-polymers1,24913
Water24,4101355
1
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7244
Polymers58,4351
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9166
Polymers58,4351
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9166
Polymers58,4351
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
C: RNA-dependent RNA polymerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)353,11032
Polymers350,6136
Non-polymers2,49826
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17800 Å2
ΔGint-416 kcal/mol
Surface area121580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.670, 196.330, 109.150
Angle α, β, γ (deg.)90.00, 114.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-694-

HOH

21A-713-

HOH

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 58435.422 Da / Num. of mol.: 3 / Fragment: UNP residues 1174-1684
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) murine norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q80J95
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1355 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 1.8M ammonium sulfate, 0.05M calcium chloride, 0.1M sodium acetate, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 17, 2009
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→29 Å / Num. all: 155383 / Num. obs: 154866 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.21 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.74 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22732 7807 5 %RANDOM
Rwork0.18626 ---
all0.18832 147059 --
obs0.18832 147059 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.649 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.04 Å2
2---0.02 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11395 0 65 1355 12815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.97616111
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42251465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11222.987549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.578152048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.80515114
X-RAY DIFFRACTIONr_chiral_restr0.0950.21701
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219091
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5791.57226
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.769211671
X-RAY DIFFRACTIONr_scbond_it4.62934645
X-RAY DIFFRACTIONr_scangle_it7.1684.54421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 590 -
Rwork0.285 10847 -
obs--99.81 %

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