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- PDB-3upf: Crystal structure of murine norovirus RNA-dependent RNA polymeras... -

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Basic information

Entry
Database: PDB / ID: 3upf
TitleCrystal structure of murine norovirus RNA-dependent RNA polymerase bound to NF023
ComponentsRNA-dependent RNA polymerase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / murine norovirus / RNA-dependent RNA polymerase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Chem-0BU / Genome polyprotein
Similarity search - Component
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 18, 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)182,37313
Polymers178,6073
Non-polymers3,76510
Water11,259625
1
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6633
Polymers59,5361
Non-polymers1,1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7594
Polymers59,5361
Non-polymers1,2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9516
Polymers59,5361
Non-polymers1,4155
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)364,74526
Polymers357,2146
Non-polymers7,53120
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15380 Å2
ΔGint-259 kcal/mol
Surface area121470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.860, 195.950, 109.240
Angle α, β, γ (deg.)90.00, 114.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 59535.738 Da / Num. of mol.: 3 / Fragment: UNP residues 1174-1684
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80J95
#2: Chemical ChemComp-0BU / 8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid / NF023


Mass: 1030.985 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H26N4O21S6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 1.5 M ammonium sulfate, 11 % glycerol, 50 mM 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: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2011
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. all: 70871 / Num. obs: 70871 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.74 Å / % possible all: 100

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Processing

Software
NameVersionClassification
xCUBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 22.969 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26062 3578 5 %RANDOM
Rwork0.1985 ---
all0.20167 67276 --
obs0.20167 67276 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.82 Å2
2--0.5 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11376 0 233 625 12234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211900
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.99316165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51351419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09523.117539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.158152011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.75415108
X-RAY DIFFRACTIONr_chiral_restr0.0810.21697
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219099
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_it1.1781.57141
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.246211507
X-RAY DIFFRACTIONr_scbond_it3.59934759
X-RAY DIFFRACTIONr_scangle_it5.6244.54657
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 256 -
Rwork0.289 4954 -
obs--99.98 %
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)
10.54180.0665-0.11110.28340.33920.40680.08980.0235-0.02470.0381-0.0401-0.05930.0108-0.0615-0.04970.08210.0497-0.02250.09020.01740.011915.91-49.95433.149
20.03810.0879-0.0080.4056-0.34760.4930.0012-0.0197-0.0009-0.01710.0217-0.0226-0.008-0.0186-0.02290.09550.03730.02170.0730.01860.056936.181-46.883-11.116
30.1985-0.0277-0.04350.2665-0.18560.2321-0.00650.00860.02390.00850.0062-0.010.01560.00140.00030.12950.020.03010.06120.00050.0467-7.1430.35823.143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 488
2X-RAY DIFFRACTION1A600
3X-RAY DIFFRACTION2B2 - 488
4X-RAY DIFFRACTION2B600
5X-RAY DIFFRACTION3C5 - 488
6X-RAY DIFFRACTION3C600

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