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- PDB-5dg6: 2.35A resolution structure of Norovirus 3CL protease in complex a... -

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Basic information

Entry
Database: PDB / ID: 5dg6
Title2.35A resolution structure of Norovirus 3CL protease in complex an oxadiazole-based, cell permeable macrocyclic (21-mer) inhibitor
Components3C-LIKE PROTEASE
KeywordsHYDROLASE/HYDROLASE Inhibitor / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / OXADIAZOLE INHIBITOR / CELL PERMEABLE / 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 / 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
tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-23-oxa-6,9,14,21,22-pentaazabicyclo[18.2.1]tricosa-1(22),20-dien-4-yl]carbamate / Chem-V66 / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Damalanka, V.C. / Kim, Y. / Alliston, K.R. / Weerawarna, P.M. / Kankanamalage, A.C.G. / Lushington, G.H. / 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)R01 AI109039 United States
CitationJournal: J.Med.Chem. / Year: 2016
Title: Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 3CL Protease.
Authors: Damalanka, V.C. / Kim, Y. / Alliston, K.R. / Weerawarna, P.M. / Galasiti Kankanamalage, A.C. / Lushington, G.H. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Sep 27, 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 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Aug 12, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 1.6Sep 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: 3C-LIKE PROTEASE
B: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9656
Polymers40,2522
Non-polymers7134
Water99155
1
A: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8044
Polymers20,1261
Non-polymers6783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1622
Polymers20,1261
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.686, 67.113, 127.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3C-LIKE PROTEASE


Mass: 20126.131 Da / Num. of mol.: 2 / Fragment: UNP residues 1101-1281
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 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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-V66 / tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-23-oxa-6,9,14,21,22-pentaazabicyclo[18.2.1]tricosa-1(22),20-dien-4-yl]carbamate


Type: Peptide-like / Class: Inhibitor / Mass: 606.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H50N6O7
References: tert-butyl [(4S,7S,10S)-7-(cyclohexylmethyl)-10-(hydroxymethyl)-5,8,13-trioxo-23-oxa-6,9,14,21,22-pentaazabicyclo[18.2.1]tricosa-1(22),20-dien-4-yl]carbamate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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 Å3/Da / Density % sol: 38.57 %
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: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→42.49 Å / Num. obs: 14146 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 30.32 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 9.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.4data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR9

3ur9


Resolution: 2.35→35.9 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 712 5.05 %
Rwork0.209 --
obs0.212 14091 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.52 Å2
Refinement stepCycle: LAST / Resolution: 2.35→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 46 55 2437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072438
X-RAY DIFFRACTIONf_angle_d0.9183319
X-RAY DIFFRACTIONf_dihedral_angle_d11.9711411
X-RAY DIFFRACTIONf_chiral_restr0.053386
X-RAY DIFFRACTIONf_plane_restr0.007415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.53150.31811350.26012615X-RAY DIFFRACTION100
2.5315-2.78610.3431470.2582606X-RAY DIFFRACTION100
2.7861-3.18910.29141230.22982681X-RAY DIFFRACTION100
3.1891-4.0170.30951470.1882663X-RAY DIFFRACTION100
4.017-35.90430.21771600.18442814X-RAY DIFFRACTION100

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