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- PDB-4nrt: Human Norovirus polymerase bound to Compound 6 (suramin derivative) -

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Basic information

Entry
Database: PDB / ID: 4nrt
TitleHuman Norovirus polymerase bound to Compound 6 (suramin derivative)
ComponentshNV-RdRp
KeywordsVIRAL PROTEIN/TRANSCRIPTION INHIBITOR / RNA dependent RNA Polymerase / VIRAL PROTEIN-TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / 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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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-2NG / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk-like virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.022 Å
AuthorsCroci, R. / Pezzullo, M. / Tarantino, D. / Mastrangelo, E. / Milani, M. / Bolognesi, M.
CitationJournal: Plos One / Year: 2014
Title: Structural bases of norovirus RNA dependent RNA polymerase inhibition by novel suramin-related compounds.
Authors: Croci, R. / Pezzullo, M. / Tarantino, D. / Milani, M. / Tsay, S.C. / Sureshbabu, R. / Tsai, Y.J. / Mastrangelo, E. / Rohayem, J. / Bolognesi, M. / Hwu, J.R.
History
DepositionNov 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Assembly

Deposited unit
A: hNV-RdRp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2432
Polymers58,6581
Non-polymers5861
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.170, 111.950, 121.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-794-

HOH

21A-801-

HOH

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Components

#1: Protein hNV-RdRp


Mass: 58657.762 Da / Num. of mol.: 1
Fragment: RNA dependent RNA polymerase (UNP Residues 1190-1699)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk-like virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0ZNP5
#2: Chemical ChemComp-2NG / 4-({4-methyl-3-[(3-nitrobenzoyl)amino]benzoyl}amino)naphthalene-1,5-disulfonic acid


Mass: 585.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H19N3O10S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 1.2 M Na Citrate, 100 mM Na Cacodylate ph 6.2, 125 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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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 4, 2013
RadiationMonochromator: Si[111] CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.02→71.8 Å / Num. obs: 39356 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.02→2.13 Å / Rmerge(I) obs: 0.305 / % possible all: 99.1

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Processing

Software
NameVersionClassification
EDNAdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B43

2b43


Resolution: 2.022→69.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1971 5 %RANDOM
Rwork0.1638 ---
all0.1638 37385 --
obs0.1638 37954 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.022→69.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 29 494 4439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194084
X-RAY DIFFRACTIONr_bond_other_d00.023864
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9815553
X-RAY DIFFRACTIONr_angle_other_deg3.5323.0018959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59623.918171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9441525
X-RAY DIFFRACTIONr_chiral_restr0.0870.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214562
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02893
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: 2.022→2.074 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 139 -
Rwork0.245 2775 -
obs--99.08 %

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