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- PDB-6tgl: 3c-like protease from Southampton virus complexed with FMOPL000644a. -

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Basic information

Entry
Database: PDB / ID: 6tgl
Title3c-like protease from Southampton virus complexed with FMOPL000644a.
Components(Genome polyprotein) x 2
KeywordsHYDROLASE / Viral protease.
Function / homology
Function and homology information


calicivirin / 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 ...calicivirin / 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
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
Chem-LVP / PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesSouthampton virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.99 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
DepositionNov 16, 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

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2287
Polymers36,6782
Non-polymers5515
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Structure suggests tetrameric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-15 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.880, 89.200, 61.180
Angle α, β, γ (deg.)90.000, 97.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-414-

HOH

31B-415-

HOH

41B-433-

HOH

51B-450-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 304 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-LVP / ~{N}'-(2-fluorophenyl)-1,2-oxazole-5-carbohydrazide


Mass: 221.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8FN3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: Protein concentration 4 mg/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: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.99→25.11 Å / Num. obs: 22739 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.067 / Rrim(I) all: 0.123 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.99-2.043.10.4482.816820.6680.2980.5498.9
8.9-25.13.50.03627.82510.9970.0230.04393.2

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6t1q

6t1q


Resolution: 1.99→25.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.258 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1902 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.178
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1113 4.9 %RANDOM
Rwork0.1698 ---
obs0.173 21625 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.62 Å2 / Biso mean: 28.552 Å2 / Biso min: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0 Å20.43 Å2
2---0.25 Å20 Å2
3---1.51 Å2
Refinement stepCycle: final / Resolution: 1.99→25.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 33 299 2902
Biso mean--54.99 41.39 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172609
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6433727
X-RAY DIFFRACTIONr_angle_other_deg1.221.576030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4135363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.75119.573117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91715441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0731520
X-RAY DIFFRACTIONr_chiral_restr0.0630.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 89 -
Rwork0.234 1592 -
all-1681 -
obs--98.82 %

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