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- PDB-5e0h: 1.95 A resolution structure of Norovirus 3CL protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 5e0h
Title1.95 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic (18-mer) inhibitor
ComponentsNorovirus 3C-like protease
KeywordsPROTEASE/PROTEASE INHIBITOR / protease / norovirus / norwalk virus / antiviral inhibitors / triazole macrocyclic inhibitor / cell permeable / PROTEASE-PROTEASE INHIBITOR complex
Function / homology
Function and homology information


calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
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 / 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 / Trypsin-like serine proteases ...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 / 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 / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
(phenylmethyl) ~{N}-[(9~{S},12~{S},15~{S})-9-(hydroxymethyl)-12-(2-methylpropyl)-6,11,14-tris(oxidanylidene)-1,5,10,13,18,19-hexazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate / Chem-5LH / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Weerawarna, P.M. / Kim, Y. / Kankanamalage, A.C.G. / Damalanka, V.C. / Lushington, G.H. / Alliston, K.R. / Chang, K.-O. / Groutas, W.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI109039 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Structure-based design and synthesis of triazole-based macrocyclic inhibitors of norovirus protease: Structural, biochemical, spectroscopic, and antiviral studies.
Authors: Weerawarna, P.M. / Kim, Y. / Galasiti Kankanamalage, A.C. / Damalanka, V.C. / Lushington, G.H. / Alliston, K.R. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionSep 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Norovirus 3C-like protease
B: Norovirus 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9024
Polymers40,2522
Non-polymers6502
Water1,69394
1
A: Norovirus 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6842
Polymers20,1261
Non-polymers5581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Norovirus 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2182
Polymers20,1261
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.102, 48.772, 53.083
Angle α, β, γ (deg.)94.000, 109.500, 101.290
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Norovirus 3C-like protease


Mass: 20126.131 Da / Num. of mol.: 2 / Fragment: UNP residues 1101-1281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q83883, calicivirin
#2: Chemical ChemComp-5LH / (phenylmethyl) ~{N}-[(9~{S},12~{S},15~{S})-9-(hydroxymethyl)-12-(2-methylpropyl)-6,11,14-tris(oxidanylidene)-1,5,10,13,18,19-hexazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 557.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H39N7O6
References: (phenylmethyl) ~{N}-[(9~{S},12~{S},15~{S})-9-(hydroxymethyl)-12-(2-methylpropyl)-6,11,14-tris(oxidanylidene)-1,5,10,13,18,19-hexazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.24 Å3/Da / Density % sol: 45.12 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG3350, 200 mM sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→37.01 Å / Num. obs: 24256 / % possible obs: 95.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 29.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Net I/σ(I): 8 / Num. measured all: 43724
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.95-21.80.4421.7303117120.7550.44294
8.94-37.011.90.022224852500.9980.02295.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.93 Å37.01 Å
Translation3.93 Å37.01 Å

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UR9

3ur9


Resolution: 1.95→37.01 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1244 5.13 %
Rwork0.1826 22998 -
obs0.1846 24242 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.47 Å2 / Biso mean: 38.5726 Å2 / Biso min: 17.81 Å2
Refinement stepCycle: final / Resolution: 1.95→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 39 94 2519
Biso mean--37.44 38.92 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112498
X-RAY DIFFRACTIONf_angle_d1.1363404
X-RAY DIFFRACTIONf_chiral_restr0.062392
X-RAY DIFFRACTIONf_plane_restr0.008429
X-RAY DIFFRACTIONf_dihedral_angle_d12.2631446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.02810.29951350.24642533266894
2.0281-2.12040.30021450.22192536268194
2.1204-2.23220.26511270.20222552267995
2.2322-2.3720.221270.19812526265395
2.372-2.55510.24261420.18832594273696
2.5551-2.81210.25231280.19262569269796
2.8121-3.21890.23381460.19212576272296
3.2189-4.05460.22391460.17122564271096
4.0546-37.01860.1671480.16082548269695

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