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- PDB-6bic: 2.25 A resolution structure of Norovirus 3CL protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 6bic
Title2.25 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
(phenylmethyl) ~{N}-[(9~{S},12~{S},15~{S})-9-(hydroxymethyl)-12-(2-methylpropyl)-6,11,14-tris(oxidanylidene)-1,5,10,13,18,19-hexazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate / Chem-5LH / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)41,3684
Polymers40,2522
Non-polymers1,1152
Water77543
1
A: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6842
Polymers20,1261
Non-polymers5581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6842
Polymers20,1261
Non-polymers5581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.602, 66.271, 125.283
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-5LH / (phenylmethyl) ~{N}-[(9~{S},12~{S},15~{S})-9-(hydroxymethyl)-12-(2-methylpropyl)-6,11,14-tris(oxidanylidene)-1,5,10,13,18,19-hexazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 557.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H39N7O6
References: (phenylmethyl) ~{N}-[(9~{S},12~{S},15~{S})-9-(hydroxymethyl)-12-(2-methylpropyl)-6,11,14-tris(oxidanylidene)-1,5,10,13,18,19-hexazabicyclo[15.2.1]icosa-17(20),18-dien-15-yl]carbamate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.57 % / Description: prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG2000 MME, 0.1 M potassium thiocyanate

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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: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→45.52 Å / Num. obs: 15565 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 32.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.196 / Net I/σ(I): 13.5 / Num. measured all: 301166 / Scaling rejects: 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.25-2.3218.71.41814020.92199.8
9-45.5215.70.0593040.999199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.25 Å33.14 Å
Translation2.25 Å33.14 Å

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5T6D

5t6d


Resolution: 2.25→33.136 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 32.02
RfactorNum. reflection% reflection
Rfree0.2801 768 4.96 %
Rwork0.2173 --
obs0.2205 15490 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.3 Å2 / Biso mean: 40.1553 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 2.25→33.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 73 43 2471
Biso mean--48.33 33.81 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062490
X-RAY DIFFRACTIONf_angle_d0.8153390
X-RAY DIFFRACTIONf_chiral_restr0.054391
X-RAY DIFFRACTIONf_plane_restr0.005425
X-RAY DIFFRACTIONf_dihedral_angle_d12.8581419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2501-2.42370.34761460.260428633009
2.4237-2.66760.35551380.256529143052
2.6676-3.05330.32461530.242129163069
3.0533-3.84590.27671690.212829333102
3.8459-33.13910.23581620.191230963258

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