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- PDB-6w5h: 1.85 A resolution structure of Norovirus 3CL protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 6w5h
Title1.85 A resolution structure of Norovirus 3CL protease in complex with inhibitor 5d
Components3C-LIKE PROTEASE
KeywordsHYDROLASE/HYDROLASE Inhibitor / PROTEASE / Norovirus 3CL protease / Inhhibitors / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / host cell perinuclear region of cytoplasm / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / host cell perinuclear region of cytoplasm / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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 / RNA-directed RNA polymerase, C-terminal domain ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate / Chem-TKP / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rathnayake, A.D. / Kim, Y. / Chang, K.O. / Groutas, W.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI109039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structure-Guided Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease.
Authors: Rathnayake, A.D. / Kim, Y. / Dampalla, C.S. / Nguyen, H.N. / Jesri, A.M. / Kashipathy, M.M. / Lushington, G.H. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionMar 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 1.2Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-LIKE PROTEASE
B: 3C-LIKE PROTEASE
C: 3C-LIKE PROTEASE
D: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0688
Polymers79,9804
Non-polymers2,0884
Water2,648147
1
A: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5172
Polymers19,9951
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5172
Polymers19,9951
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5172
Polymers19,9951
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5172
Polymers19,9951
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.943, 38.028, 115.241
Angle α, β, γ (deg.)92.310, 98.310, 96.640
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3C-LIKE PROTEASE


Mass: 19994.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine tag
Source: (gene. exp.) Norwalk virus (strain GI/Human/United States/Norwalk/1968)
Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q83883, calicivirin
#2: Chemical
ChemComp-TKP / 2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate


Type: Peptide-like / Class: Inhibitor / Mass: 522.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H40ClN3O5 / Feature type: SUBJECT OF INVESTIGATION
References: 2-(3-chlorophenyl)-2-methylpropyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% w/v PEG 2000 MME, 0.1 M Tris, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→37.95 Å / Num. obs: 50861 / % possible obs: 96.8 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.8 / Num. measured all: 178212 / Scaling rejects: 3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.759 / Num. measured all: 10940 / Num. unique obs: 3063 / CC1/2: 0.784 / Net I/σ(I) obs: 1.8 / % possible all: 95.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.25 Å113.84 Å
Translation3.25 Å113.84 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PHENIXdev_3342refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR9

3ur9


Resolution: 1.85→36.433 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 2449 4.82 %
Rwork0.1827 48363 -
obs0.1846 50812 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.9 Å2 / Biso mean: 40.2077 Å2 / Biso min: 20.58 Å2
Refinement stepCycle: final / Resolution: 1.85→36.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4833 0 144 147 5124
Biso mean--40.55 43.4 -
Num. residues----663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.88780.2851350.2352278295
1.8878-1.92880.28861590.2279283096
1.9288-1.97370.28851590.2161275496
1.9737-2.0230.24641430.2016287597
2.023-2.07770.26151480.195284396
2.0777-2.13890.22691460.1816282597
2.1389-2.20790.24721360.1816283897
2.2079-2.28680.22121380.1841287197
2.2868-2.37830.23491380.1887290997
2.3783-2.48650.27321600.1958281997
2.4865-2.61760.26191540.1998285697
2.6176-2.78150.25931160.2052288797
2.7815-2.99620.2451400.1989287197
2.9962-3.29760.23541500.1965284696
3.2976-3.77430.2021590.1752284997
3.7743-4.75360.17251260.1494284596
4.7536-36.4330.2121420.1785286398

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