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- PDB-6w5k: 1.95 A resolution structure of Norovirus 3CL protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 6w5k
Title1.95 A resolution structure of Norovirus 3CL protease in complex with inhibitor 5g
Components3C-LIKE PROTEASE
KeywordsHYDROLASE/HYDROLASE Inhibitor / PROTEASE / Norovirus 3CL protease / Inhibitors / HYDROLASE / HYDROLASE-HYDROLASE 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 / cysteine-type endopeptidase activity / viral RNA genome replication ...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 / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / metal ion 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 / 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
Chem-TKV / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 1.1Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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 1.3Nov 20, 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

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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)82,0368
Polymers79,9804
Non-polymers2,0564
Water2,072115
1
A: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5092
Polymers19,9951
Non-polymers5141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5092
Polymers19,9951
Non-polymers5141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5092
Polymers19,9951
Non-polymers5141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5092
Polymers19,9951
Non-polymers5141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.697, 124.899, 64.137
Angle α, β, γ (deg.)90.000, 93.090, 90.000
Int Tables number4
Space group name H-MP1211

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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
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, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase
#2: Chemical
ChemComp-TKV / N~2~-{[2-(3-chlorophenyl)-2-methylpropoxy]carbonyl}-N-{(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide


Mass: 514.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H36ClN3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.87 Å3/Da / Density % sol: 34.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% w/v PEG3350, 0.1M Tris, 200 mM Trimethylamine N-oxide dihydrate

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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: Oct 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→44.71 Å / Num. obs: 42933 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.166 / Net I/σ(I): 7.4 / Num. measured all: 290570
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.988 / Num. measured all: 20460 / Num. unique obs: 3021 / CC1/2: 0.799 / Net I/σ(I) obs: 2.1 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.38 Å37.64 Å
Translation2.38 Å37.64 Å

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Processing

Software
NameVersionClassification
PHENIX1.18rc4_3812refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR9

3ur9


Resolution: 1.95→37.64 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2882 2192 5.11 %
Rwork0.2218 40706 -
obs0.2251 42898 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.6 Å2 / Biso mean: 33.209 Å2 / Biso min: 10.52 Å2
Refinement stepCycle: final / Resolution: 1.95→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 120 115 4887
Biso mean--32.45 32.31 -
Num. residues----642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.990.34211200.29872539265999
1.99-2.040.35321140.27842536265099
2.04-2.090.32591370.26042572270999
2.09-2.150.30351200.25825262646100
2.15-2.210.321210.23692576269799
2.21-2.280.35571500.233724822632100
2.28-2.360.29611530.2382562271599
2.36-2.460.34781600.237724852645100
2.46-2.570.28621540.230825262680100
2.57-2.70.26421490.218325472696100
2.7-2.870.28671650.219325102675100
2.87-3.090.28821510.219725362687100
3.1-3.410.30351360.209725572693100
3.41-3.90.24891150.199625682683100
3.9-4.910.22811310.18325712702100
4.91-37.640.30711160.23642613272999

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