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- PDB-6t4e: Native C3-like protease from Southampton virus complexed with FMO... -

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Basic information

Entry
Database: PDB / ID: 6t4e
TitleNative C3-like protease from Southampton virus complexed with FMOPL000287a.
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
Chem-HWH / Genome polyprotein
Similarity search - Component
Biological speciesSouthampton virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.66 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 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)37,2154
Polymers36,7752
Non-polymers4402
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Structure suggests tetrameric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.910, 89.560, 61.370
Angle α, β, γ (deg.)90.000, 96.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-393-

HOH

21A-400-

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: 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
#3: Chemical ChemComp-HWH / ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide


Mass: 220.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13FN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 47.32 %
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: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.66→25.62 Å / Num. obs: 38595 / % possible obs: 97.1 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Net I/σ(I): 12.4 / Num. measured all: 128715
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.66-1.72.90.8481.327740.4250.6131.05395.9
7.42-25.623.40.0224490.9980.0140.02695.3

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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 / Resolution: 1.66→25.62 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.512 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.1
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; ANISOTROPIC U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 1888 4.9 %RANDOM
Rwork0.1371 ---
obs0.1408 36705 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.31 Å2 / Biso mean: 27.922 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.36 Å2
2---0.25 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 1.66→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 32 232 2841
Biso mean--48.92 41.3 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132688
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172562
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.643654
X-RAY DIFFRACTIONr_angle_other_deg1.3721.575918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6335346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.83319.735113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09815428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6561518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
X-RAY DIFFRACTIONr_rigid_bond_restr3.43135248
LS refinement shellResolution: 1.66→1.703 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 131 -
Rwork0.279 2632 -
all-2763 -
obs--95.7 %

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