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- PDB-5e0j: 1.20 A resolution structure of Norovirus 3CL protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 5e0j
Title1.20 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic (21-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 Golgi 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 / viral RNA genome replication / cysteine-type endopeptidase activity ...calicivirin / host cell Golgi 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 / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / membrane / metal ion binding
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}-[(12~{S},15~{S},18~{S})-15-(cyclohexylmethyl)-12-(hydroxymethyl)-9,14,17-tris(oxidanylidene)-1,8,13,16,21,22-hexazabicyclo[18.2.1]tricosa-20(23),21-dien-18-yl]carbamate / Chem-5LJ / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,8725
Polymers20,1261
Non-polymers7464
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-24 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.666, 37.159, 61.859
Angle α, β, γ (deg.)90.000, 110.040, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

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Components

#1: Protein Norovirus 3C-like protease


Mass: 20126.131 Da / Num. of mol.: 1 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-5LJ / (phenylmethyl) ~{N}-[(12~{S},15~{S},18~{S})-15-(cyclohexylmethyl)-12-(hydroxymethyl)-9,14,17-tris(oxidanylidene)-1,8,13,16,21,22-hexazabicyclo[18.2.1]tricosa-20(23),21-dien-18-yl]carbamate


Type: peptide-like, Polypeptide / Class: Inhibitor / Mass: 639.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H49N7O6
References: (phenylmethyl) ~{N}-[(12~{S},15~{S},18~{S})-15-(cyclohexylmethyl)-12-(hydroxymethyl)-9,14,17-tris(oxidanylidene)-1,8,13,16,21,22-hexazabicyclo[18.2.1]tricosa-20(23),21-dien-18-yl]carbamate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.79 Å3/Da / Density % sol: 31.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG 2000 MME, 150 mM potassium bromide

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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: Nov 18, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→32.63 Å / Num. obs: 42941 / % possible obs: 96.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 12.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.025 / Net I/σ(I): 16.3 / Num. measured all: 246169 / Scaling rejects: 146
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.2-1.223.60.7871.9717720160.6880.47693.7
6.57-32.636.30.04348.818572970.9950.01998.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.32 Å58.09 Å
Translation1.32 Å58.09 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UR9

3ur9


Resolution: 1.2→31.957 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 16.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1654 2020 4.71 %
Rwork0.1365 40906 -
obs0.1379 42926 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.45 Å2 / Biso mean: 19.1086 Å2 / Biso min: 7.6 Å2
Refinement stepCycle: final / Resolution: 1.2→31.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 49 170 1492
Biso mean--23.11 30.5 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091382
X-RAY DIFFRACTIONf_angle_d1.0871883
X-RAY DIFFRACTIONf_chiral_restr0.081214
X-RAY DIFFRACTIONf_plane_restr0.007238
X-RAY DIFFRACTIONf_dihedral_angle_d12.768489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.230.23541290.21362832296193
1.23-1.26330.22451340.19582819295394
1.2633-1.30050.21021360.17622814295094
1.3005-1.34240.18621570.16092829298694
1.3424-1.39040.19971330.14652887302095
1.3904-1.44610.18841410.13422904304596
1.4461-1.51190.15361490.11612899304896
1.5119-1.59160.13931420.11152960310297
1.5916-1.69130.16071460.11462907305397
1.6913-1.82190.14331410.12842979312097
1.8219-2.00520.15881490.12582989313898
2.0052-2.29530.16071420.12982985312798
2.2953-2.89150.1631580.14562998315698
2.8915-31.96880.16381630.13553104326799

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