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- PDB-8cnx: Structure of Enterovirus D68 3C protease -

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Basic information

Entry
Database: PDB / ID: 8cnx
TitleStructure of Enterovirus D68 3C protease
ComponentsProtease 3C
KeywordsANTIVIRAL PROTEIN / Enterovirus 3C protease ASAP AViDD Cysteine
Function / homology
Function and homology information


symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / monoatomic ion transmembrane transport / symbiont-mediated suppression of host NF-kappaB cascade / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / 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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
Biological speciesEnterovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsLithgo, R.M. / Fairhead, M. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Godoy, A.S. / Marples, P.G. / Ni, X. / Tomlinson, C.W.E. / Wild, C. ...Lithgo, R.M. / Fairhead, M. / Koekemoer, L. / Aschenbrenner, J.C. / Balcomb, B.H. / Godoy, A.S. / Marples, P.G. / Ni, X. / Tomlinson, C.W.E. / Wild, C. / Fearon, D. / Walsh, M.A. / von Delft, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171399 United States
CitationJournal: To Be Published
Title: Structure of EV D68 3C protease
Authors: Lithgo, R.M. / von Delft, F.
History
DepositionFeb 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease 3C
B: Protease 3C


Theoretical massNumber of molelcules
Total (without water)42,6272
Polymers42,6272
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area15850 Å2
Unit cell
Length a, b, c (Å)42.820, 62.530, 147.360
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 Protease 3C / Picornain 3C / P3C


Mass: 21313.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q68T42, picornain 3C
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.14 / Details: 25% PEG 3,350 0.1 M Tris 0.2 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 1.49→38.63 Å / Num. obs: 60463 / % possible obs: 91.9 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.4
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 11079 / CC1/2: 0.388 / % possible all: 56.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→38.627 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.222 / SU ML: 0.074 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2199 3016 4.995 %
Rwork0.2036 57368 -
all0.204 --
obs-60384 92.043 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.167 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0 Å2
2--2.642 Å20 Å2
3----1.441 Å2
Refinement stepCycle: LAST / Resolution: 1.49→38.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 0 313 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122916
X-RAY DIFFRACTIONr_bond_other_d0.0360.0162658
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6553966
X-RAY DIFFRACTIONr_angle_other_deg0.9021.5646181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3125376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.348521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63710478
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.85610133
X-RAY DIFFRACTIONr_chiral_restr0.080.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_nbd_refined0.2250.2368
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22069
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21389
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2203
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2820.28
X-RAY DIFFRACTIONr_nbd_other0.1960.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3210.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1430.21
X-RAY DIFFRACTIONr_mcbond_it2.6662.5761471
X-RAY DIFFRACTIONr_mcbond_other2.6422.5751471
X-RAY DIFFRACTIONr_mcangle_it3.5233.8551843
X-RAY DIFFRACTIONr_mcangle_other3.5253.8571844
X-RAY DIFFRACTIONr_scbond_it3.5182.9671445
X-RAY DIFFRACTIONr_scbond_other3.5172.9681446
X-RAY DIFFRACTIONr_scangle_it5.244.2942118
X-RAY DIFFRACTIONr_scangle_other5.2384.2962119
X-RAY DIFFRACTIONr_lrange_it6.52637.1123046
X-RAY DIFFRACTIONr_lrange_other6.51134.3792975
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.49-1.5290.4421410.44925650.44947710.7590.76256.71770.459
1.529-1.570.4091410.40528850.40646390.8180.80865.22960.406
1.57-1.6160.3651700.36632930.36645300.8550.84676.44590.357
1.616-1.6660.3121920.3337450.32944050.8840.89489.37570.311
1.666-1.720.3022120.29240910.29343030.9060.921000.265
1.72-1.780.2762230.25939230.2641460.9310.9441000.233
1.78-1.8470.2672010.2437930.24239940.930.9541000.218
1.847-1.9230.2551860.2236560.22238420.9560.9641000.201
1.923-2.0080.2591670.22335360.22437040.9480.96199.9730.207
2.008-2.1060.2261980.19933650.235630.9640.9721000.188
2.106-2.2190.2121910.19931810.233720.9670.9741000.192
2.219-2.3530.2131410.17830790.1832200.9720.9791000.177
2.353-2.5150.1891460.17528930.17630390.9760.9811000.177
2.515-2.7160.211520.18126860.18228380.9730.981000.189
2.716-2.9730.2021260.18224700.18325960.9770.9791000.196
2.973-3.3220.2061240.17822600.17923840.9720.981000.199
3.322-3.8310.1831040.18120060.18121100.9810.9811000.208
3.831-4.6810.177850.16517330.16618180.9790.9821000.205
4.681-6.5710.245660.20213700.20314360.9720.9791000.262
6.571-38.6270.184500.2398380.2358900.9780.95899.77530.369

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