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

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Basic information

Entry
Database: PDB / ID: 6bib
Title1.95 A resolution structure of Norovirus 3CL protease in complex with a triazole-based macrocyclic inhibitor
Components3C-like protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / norovirus / Norwalk virus / antiviral inhibitors / triazole-based macrocyclic inhibitor / 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
Chem-DW7 / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Kankanamalage, A.C.G. / Weerawarna, P.M. / 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)AI109039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: Proteins / Year: 2019
Title: Putative structural rearrangements associated with the interaction of macrocyclic inhibitors with norovirus 3CL protease.
Authors: Galasiti Kankanamalage, A.C. / Weerawarna, P.M. / Rathnayake, A.D. / Kim, Y. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionNov 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: 3C-like protease
B: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4484
Polymers40,2522
Non-polymers1,1952
Water2,720151
1
A: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7242
Polymers20,1261
Non-polymers5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7242
Polymers20,1261
Non-polymers5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.873, 67.191, 126.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
Source: (gene. exp.) Norwalk virus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q83883, calicivirin
#2: Chemical ChemComp-DW7 / benzyl [(9S,12S,15S)-12-(cyclohexylmethyl)-9-(hydroxymethyl)-6,11,14-trioxo-1,5,10,13,18,19-hexaazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate


Mass: 597.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H43N7O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 38.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% w/v PEG3350, 0.1 M HEPES

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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: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.07 Å / Num. obs: 24414 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.95-26.40.8731101617110.7912.5100
8.94-46.075.60.05717783170.99723.699.5

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5T6D

5t6d


Resolution: 1.95→46.069 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2399 1246 5.12 %
Rwork0.1846 --
obs0.1875 24353 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.9 Å2 / Biso mean: 26.2666 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: final / Resolution: 1.95→46.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 79 151 2643
Biso mean--33.49 30.77 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112592
X-RAY DIFFRACTIONf_angle_d1.1623530
X-RAY DIFFRACTIONf_chiral_restr0.064403
X-RAY DIFFRACTIONf_plane_restr0.008445
X-RAY DIFFRACTIONf_dihedral_angle_d11.9451498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-2.02810.31771460.237225272673
2.0281-2.12040.22731130.210325352648
2.1204-2.23220.30291340.197325272661
2.2322-2.3720.2541270.191725372664
2.372-2.55520.26561260.186525412667
2.5552-2.81230.22781530.184825512704
2.8123-3.21910.25151500.183625642714
3.2191-4.05540.23241400.172225952735
4.0554-46.08220.20671570.171427302887

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