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- PDB-5t6f: 1.90 A resolution structure of Norovirus 3CL protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 5t6f
Title1.90 A resolution structure of Norovirus 3CL protease in complex with the dipeptidyl inhibitor 7l (orthorhombic P form)
ComponentsGenome polyprotein
KeywordsPROTEASE/PROTEASE INHIBITOR / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / DIPEPTIDYL INHIBITOR / PROTEASE-PROTEASE 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-N38 / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Kankanamalage, A.C.G. / Kim, Y. / Rathnayake, A.D. / Damalanka, V.C. / Weerawarna, P.M. / Doyle, S.T. / Alsoudi, A.F. ...Lovell, S. / Battaile, K.P. / Mehzabeen, N. / Kankanamalage, A.C.G. / Kim, Y. / Rathnayake, A.D. / Damalanka, V.C. / Weerawarna, P.M. / Doyle, S.T. / Alsoudi, A.F. / Dissanayake, D.M.P. / 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)R01AI109039 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: Structure-based exploration and exploitation of the S4 subsite of norovirus 3CL protease in the design of potent and permeable inhibitors.
Authors: Galasiti Kankanamalage, A.C. / Kim, Y. / Rathnayake, A.D. / Damalanka, V.C. / Weerawarna, P.M. / Doyle, S.T. / Alsoudi, A.F. / Dissanayake, D.M. / Lushington, G.H. / Mehzabeen, N. / ...Authors: Galasiti Kankanamalage, A.C. / Kim, Y. / Rathnayake, A.D. / Damalanka, V.C. / Weerawarna, P.M. / Doyle, S.T. / Alsoudi, A.F. / Dissanayake, D.M. / Lushington, G.H. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.5Nov 20, 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: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3324
Polymers40,2522
Non-polymers1,0792
Water1,874104
1
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6662
Polymers20,1261
Non-polymers5401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6662
Polymers20,1261
Non-polymers5401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.511, 64.801, 125.371
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 Genome polyprotein


Mass: 20126.131 Da / Num. of mol.: 2 / Fragment: Full Length (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, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase
#2: Chemical ChemComp-N38 / 3-cyclohexyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-{[3-(4-methoxyphenoxy)propyl]sulfonyl}-L- alaninamide / 3-cyclohexyl-N~2~-{[3-(4-methoxyphenoxy)propyl]sulfonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alan inamide (bound form)


Mass: 539.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H41N3O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.89 Å3/Da / Density % sol: 35.01 % / Description: Prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 200 mM sodium 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: Aug 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.05 Å / Num. obs: 24911 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 26.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.7 / Num. measured all: 158261 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Net I/σ(I) obs% possible all
1.9-1.945.80.926892615470.8342.1100
9.11-45.055.20.03414892850.99942.999.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR9

3ur9


Resolution: 1.9→35.937 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 27.58
RfactorNum. reflection% reflection
Rfree0.2489 1210 4.87 %
Rwork0.1941 --
obs0.1968 24836 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.68 Å2 / Biso mean: 35.388 Å2 / Biso min: 17.28 Å2
Refinement stepCycle: final / Resolution: 1.9→35.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 63 104 2564
Biso mean--38.25 37.23 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012529
X-RAY DIFFRACTIONf_angle_d1.0313448
X-RAY DIFFRACTIONf_chiral_restr0.065398
X-RAY DIFFRACTIONf_plane_restr0.009430
X-RAY DIFFRACTIONf_dihedral_angle_d14.6971475
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.97610.34981140.264725922706
1.9761-2.0660.28191430.236925492692
2.066-2.17490.27871400.223625802720
2.1749-2.31120.2821240.216325922716
2.3112-2.48960.26951240.212226202744
2.4896-2.740.29051460.218825862732
2.74-3.13630.27391390.194126472786
3.1363-3.95060.23511320.173826562788
3.9506-35.94330.20011480.171928042952

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