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- PDB-6t4s: 3C-like protease from Southampton virus complexed with FMOPL000013a. -

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Basic information

Entry
Database: PDB / ID: 6t4s
Title3C-like protease from Southampton virus complexed with FMOPL000013a.
Components(Genome polyprotein) x 2
KeywordsHYDROLASE / Viral protease.
Function / homology
Function and homology information


calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion 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 / RNA-directed RNA polymerase, C-terminal domain ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2-(trifluoromethoxy)benzoic acid / Genome polyprotein
Similarity search - Component
Biological speciesSouthampton virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.02 Å
AuthorsGuo, J. / Cooper, J.B.
CitationJournal: J Struct Biol X / Year: 2020
Title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors.
Authors: Guo, J. / Douangamath, A. / Song, W. / Coker, A.R. / Chan, A.W.E. / Wood, S.P. / Cooper, J.B. / Resnick, E. / London, N. / Delft, F.V.
History
DepositionOct 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8843
Polymers36,6782
Non-polymers2061
Water5,026279
1
A: Genome polyprotein
B: Genome polyprotein
hetero molecules

A: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7676
Polymers73,3554
Non-polymers4122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Buried area6000 Å2
ΔGint-40 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.892, 89.997, 60.960
Angle α, β, γ (deg.)90.000, 97.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

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Components

#1: Protein Genome polyprotein


Mass: 18387.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Southampton virus (serotype 3) / Gene: ORF1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase
#2: Protein Genome polyprotein


Mass: 18290.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Southampton virus (serotype 3) / Gene: ORF1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase
#3: Chemical ChemComp-K2P / 2-(trifluoromethoxy)benzoic acid


Mass: 206.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5F3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: Protein concentration 4mg/ml. 0.2 M ammonium citrate and 12% (v/v) PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.02→60.51 Å / Num. obs: 21956 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.096 / Rrim(I) all: 0.178 / Net I/σ(I): 5.3 / Num. measured all: 73672 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.02-2.073.31.131.615830.5090.7291.34898.9
9.03-60.513.60.07812.32600.9890.0460.09199.8

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6t1q

6t1q


Resolution: 2.02→60.5 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.13 / SU ML: 0.213 / SU R Cruickshank DPI: 0.2432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.229
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2999 1049 4.8 %RANDOM
Rwork0.2136 ---
obs0.2177 20829 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.63 Å2 / Biso mean: 31.099 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.02 Å2
2---0.01 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.02→60.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 14 279 2863
Biso mean--52.58 41.39 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132645
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172516
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.6413591
X-RAY DIFFRACTIONr_angle_other_deg1.2621.575809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4565341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.2620108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89215424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9221518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
LS refinement shellResolution: 2.02→2.072 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.385 76 -
Rwork0.336 1482 -
obs--97.31 %

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