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- PDB-5tg2: 1.75 A resolution structure of Norovirus 3CL protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 5tg2
Title1.75 A resolution structure of Norovirus 3CL protease in complex with the a n-pentyl substituted macrocyclic inhibitor (17-mer)
Components3C-LIKE PROTEASE
KeywordsPROTEASE/PROTEASE INHIBITOR / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / MACROCYCLIC INHIBITOR / HYDROLASE-HYDROLASE inhibitor complex / PROTEASE-PROTEASE INHIBITOR complex
Function / homology
Function and homology information


calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP 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 / 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
(4S,7S,17R)-7-(hydroxymethyl)-4-(2-methylpropyl)-17-pentyl-1-oxa-3,6,11-triazacycloheptadecane-2,5,10-trione / Chem-V69 / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Damalanka, V.C. / Kim, Y. / Kankanamalage, A.C.G. / 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)AI109039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: Eur J Med Chem / Year: 2016
Title: Design, synthesis, and evaluation of a novel series of macrocyclic inhibitors of norovirus 3CL protease.
Authors: Damalanka, V.C. / Kim, Y. / Galasiti Kankanamalage, A.C. / Lushington, G.H. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5682
Polymers20,1261
Non-polymers4421
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.020, 36.703, 61.721
Angle α, β, γ (deg.)90.000, 110.230, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

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Components

#1: Protein 3C-LIKE PROTEASE /


Mass: 20126.131 Da / Num. of mol.: 1 / 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-V69 / (4S,7S,17R)-7-(hydroxymethyl)-4-(2-methylpropyl)-17-pentyl-1-oxa-3,6,11-triazacycloheptadecane-2,5,10-trione


Type: Cyclic peptide / Class: Inhibitor / Mass: 441.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H43N3O5
References: (4S,7S,17R)-7-(hydroxymethyl)-4-(2-methylpropyl)-17-pentyl-1-oxa-3,6,11-triazacycloheptadecane-2,5,10-trione
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.77 Å3/Da / Density % sol: 30.49 % / Description: prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% (w/v) Polyethylene glycol monomethyl ether 2,000, 100 mM Bis-Tris

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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: Aug 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→32.79 Å / Num. obs: 14350 / % possible obs: 99.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 14.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.5 / Num. measured all: 46353 / Scaling rejects: 38
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.75-1.782.40.4640.78194.6
9.09-32.793.10.0290.998199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å33.19 Å
Translation1.9 Å33.19 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.6.1phasing
PHENIXdev_2502refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E0G

5e0g


Resolution: 1.75→32.79 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.2268 710 4.95 %
Rwork0.1756 --
obs0.1781 14334 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.93 Å2 / Biso mean: 20.4205 Å2 / Biso min: 4.95 Å2
Refinement stepCycle: final / Resolution: 1.75→32.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 31 83 1299
Biso mean--22.04 29.94 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011258
X-RAY DIFFRACTIONf_angle_d0.9981705
X-RAY DIFFRACTIONf_chiral_restr0.06195
X-RAY DIFFRACTIONf_plane_restr0.007213
X-RAY DIFFRACTIONf_dihedral_angle_d14.848734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.88510.27441160.18512665278198
1.8851-2.07480.22461580.169326912849100
2.0748-2.3750.21581710.162627172888100
2.375-2.99190.2531280.187627302858100
2.9919-32.80.21291370.174428212958100

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