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- PDB-3ur0: Crystal structures of murine norovirus RNA-dependent RNA polymera... -

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Basic information

Entry
Database: PDB / ID: 3ur0
TitleCrystal structures of murine norovirus RNA-dependent RNA polymerase in complex with Suramin
ComponentsRNA-dependent RNA polymerase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / RNA-dependent RNA polymerase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


calicivirin / host cell mitochondrion / host cell endosome membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity ...calicivirin / host cell mitochondrion / host cell endosome membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / metal ion binding / membrane
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 / 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-SVR / Genome polyprotein
Similarity search - Component
Biological speciesmurine norovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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)179,87113
Polymers175,3063
Non-polymers4,56410
Water10,016556
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)59,8293
Polymers58,4351
Non-polymers1,3932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3186
Polymers58,4351
Non-polymers2,8835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: RNA-dependent RNA polymerase
hetero molecules

C: RNA-dependent RNA polymerase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)359,74126
Polymers350,6136
Non-polymers9,12920
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area19330 Å2
ΔGint-363 kcal/mol
Surface area122300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.840, 196.510, 109.070
Angle α, β, γ (deg.)90.00, 114.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA-dependent RNA polymerase


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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80J95
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN


Mass: 1297.280 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 1.3M ammonium sulfate, 10% glycerol, 0.1M TRIS, pH 8.4, 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: Apr 29, 2011
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: 2.45→48 Å / Num. all: 82297 / Num. obs: 82297 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.45→2.58 Å / % possible all: 94.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 20.235 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26831 4102 5 %RANDOM
Rwork0.19903 ---
all0.20245 78195 --
obs0.20245 78195 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.307 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20.3 Å2
2---0.45 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.45→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11334 0 141 556 12031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211771
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.98515971
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86451423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28623.097536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.371152009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.94115108
X-RAY DIFFRACTIONr_chiral_restr0.0890.21685
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219002
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_it1.4231.57127
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.617211490
X-RAY DIFFRACTIONr_scbond_it4.43434644
X-RAY DIFFRACTIONr_scangle_it6.7614.54476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.452→2.516 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 282 -
Rwork0.283 5336 -
obs--90.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.62450.18720.05471.1247-0.61351.05710.0102-0.07420.07840.00610.0118-0.0446-0.06960.0028-0.0220.06480.07340.03070.13470.03110.0956-24.29650.817-10.745
21.1671-0.197-0.45181.73281.28151.56980.0918-0.0201-0.00820.04070.0206-0.13450.05170.0176-0.11240.11260.0644-0.04610.19260.04370.0478-44.86747.90633.049
30.68130.02070.05830.8676-0.29320.7137-0.00760.01450.00270.0650.0399-0.0164-0.01110.0322-0.03230.11770.02340.0160.089-0.00720.0114-7.094-0.1423.004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 488
2X-RAY DIFFRACTION1A516 - 518
3X-RAY DIFFRACTION1A519 - 691
4X-RAY DIFFRACTION2B2 - 488
5X-RAY DIFFRACTION2B516 - 517
6X-RAY DIFFRACTION2B518 - 683
7X-RAY DIFFRACTION3C4 - 488
8X-RAY DIFFRACTION3C516 - 520
9X-RAY DIFFRACTION3C521 - 737

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