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- PDB-6w5l: 2.1 A resolution structure of Norovirus 3CL protease in complex w... -

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Basic information

Entry
Database: PDB / ID: 6w5l
Title2.1 A resolution structure of Norovirus 3CL protease in complex with inhibitor 7g
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
Chem-T0D / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 2.0Nov 4, 2020Group: Database references / Non-polymer description / Category: chem_comp / citation
Item: _chem_comp.formula / _citation.journal_volume ..._chem_comp.formula / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.1Oct 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 2.2Oct 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)82,9498
Polymers80,5324
Non-polymers2,4164
Water1,45981
1
A: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7372
Polymers20,1331
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7372
Polymers20,1331
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7372
Polymers20,1331
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7372
Polymers20,1331
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.435, 37.859, 115.535
Angle α, β, γ (deg.)91.650, 96.440, 95.440
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3C-LIKE PROTEASE


Mass: 20133.080 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-T0D / (2~{S})-~{N}-[(1~{R})-1-[bis($l^{1}-oxidanyl)-methoxy-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[[2-(3-chlorophenyl)-2-methyl-propoxy]-oxidanylidene-methyl]amino]-4-methyl-pentanamide


Mass: 604.113 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H38ClN3O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (w/v) PEG 3350, 0.1M Tris, 200 mM ammonium acetate

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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: 2.1→38.24 Å / Num. obs: 35582 / % possible obs: 97.2 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.9 / Num. measured all: 124871
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.714 / Num. measured all: 9827 / Num. unique obs: 2858 / CC1/2: 0.856 / Net I/σ(I) obs: 1.8 / % possible all: 96.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.25 Å114.72 Å
Translation3.25 Å114.72 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: 2.1→36.21 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 34.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 1685 4.75 %
Rwork0.2038 33799 -
obs0.2068 35484 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.05 Å2 / Biso mean: 47.9256 Å2 / Biso min: 25.68 Å2
Refinement stepCycle: final / Resolution: 2.1→36.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 132 81 5025
Biso mean--50.99 45.83 -
Num. residues----660
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.16180.2931400.2432275596
2.1618-2.23160.29691490.2504283596
2.2316-2.31130.3071370.2446281497
2.3113-2.40380.33711310.2434278096
2.4038-2.51320.30421380.2467287597
2.5132-2.64570.32731170.2467279797
2.6457-2.81140.30891320.2409282097
2.8114-3.02830.28091590.2215281298
3.0283-3.33290.26541610.22281297
3.3329-3.81470.27241400.1963283697
3.8147-4.80440.22021460.1618280897
4.8044-36.210.24131350.1781285598

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