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- PDB-4lq3: Crystal structure of human norovirus RNA-dependent RNA-polymerase... -

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Basic information

Entry
Database: PDB / ID: 4lq3
TitleCrystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDS
Components
  • 5'-R(P*GP*G)-3'
  • RNA-dependent RNA-polymerase
KeywordsVIRAL PROTEIN/REPLICATION INHIBITOR/RNA / RNA-dependent-RNA-polymerase / RdRp-inhibotir complex / VIRAL PROTEIN-REPLICATION INHIBITOR-RNA complex
Function / homology
Function and homology information


helicase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helix non-globular / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / 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. / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-20V / RNA / Genome polyprotein
Similarity search - Component
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMilani, M. / Tarantino, D. / Mastrangelo, E. / Croci, R.
CitationJournal: Antiviral Res. / Year: 2014
Title: Naphthalene-sulfonate inhibitors of human norovirus RNA-dependent RNA-polymerase.
Authors: Tarantino, D. / Pezzullo, M. / Mastrangelo, E. / Croci, R. / Rohayem, J. / Robel, I. / Bolognesi, M. / Milani, M.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Structure summary
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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
R: 5'-R(P*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7537
Polymers59,3032
Non-polymers2,4505
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-11 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.750, 116.100, 122.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein RNA-dependent RNA-polymerase


Mass: 58657.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q2N379
#2: RNA chain 5'-R(P*GP*G)-3'


Mass: 645.454 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: 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.: 4 / Source method: obtained synthetically / Formula: C18H15N4O14PS2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 1.2M sodium citrate, 0.1M sodium cacodylate, 0.125M sodium chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2013
RadiationMonochromator: silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.6→38.4 Å / Num. all: 19046 / Num. obs: 19046 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.66 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.4 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.092 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28535 985 5.2 %RANDOM
Rwork0.21993 ---
obs0.22321 18061 99.61 %-
all-18061 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.007 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---1.33 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 46 157 132 4215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024189
X-RAY DIFFRACTIONr_bond_other_d00.023835
X-RAY DIFFRACTIONr_angle_refined_deg1.1832.0045715
X-RAY DIFFRACTIONr_angle_other_deg3.5383.0028880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65724.012167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79115690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8031524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214578
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02890
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 68 -
Rwork0.352 1308 -
obs--99.49 %

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