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- PDB-9ax9: Crystal Structure of Enterovirus 68 3C Protease C147A Mutant with... -

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Basic information

Entry
Database: PDB / ID: 9ax9
TitleCrystal Structure of Enterovirus 68 3C Protease C147A Mutant with 3B3C peptide at 2.00 Angstroms
Components
  • 3B3C peptide
  • Protease 3C
KeywordsVIRAL PROTEIN / HYDROLASE / PROTEASE / ENTEROVIRUS / 3C PROTEIN / EV68 / INHIBITOR
Function / homology
Function and homology information


picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated suppression of host innate immune response / 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 / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 speciesHuman enterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAzzolino, V.N. / Shaqra, A.M. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F30AI181515-01 United States
CitationJournal: Viruses / Year: 2024
Title: Elucidating the Substrate Envelope of Enterovirus 68-3C Protease: Structural Basis of Specificity and Potential Resistance.
Authors: Azzolino, V.N. / Shaqra, A.M. / Ali, A. / Kurt Yilmaz, N. / Schiffer, C.A.
History
DepositionMar 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease 3C
B: Protease 3C
C: 3B3C peptide


Theoretical massNumber of molelcules
Total (without water)40,7673
Polymers40,7673
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.784, 103.343, 43.213
Angle α, β, γ (deg.)90.000, 110.800, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Protease 3C


Mass: 20083.779 Da / Num. of mol.: 2 / Mutation: C147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus D68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2K8BQT2, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein/peptide 3B3C peptide


Mass: 599.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus D68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M BisTris Propane 0.2M Potassium Thiocyanate PEG3350 12-30%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→31.83 Å / Num. obs: 21924 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 32.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.029 / Rrim(I) all: 0.041 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2200 / CC1/2: 0.942 / Rpim(I) all: 0.163 / Rrim(I) all: 0.231 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
Coot0.9.8.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.19 Å / SU ML: 0.2048 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.5573
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2282 1097 5.01 %
Rwork0.1808 20821 -
obs0.1833 21918 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.98 Å2
Refinement stepCycle: LAST / Resolution: 2→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 0 230 2987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022850
X-RAY DIFFRACTIONf_angle_d0.48243887
X-RAY DIFFRACTIONf_chiral_restr0.0453447
X-RAY DIFFRACTIONf_plane_restr0.0074510
X-RAY DIFFRACTIONf_dihedral_angle_d4.9869405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.30621370.22332603X-RAY DIFFRACTION99.89
2.09-2.20.30691360.20932601X-RAY DIFFRACTION99.82
2.2-2.340.26491380.20022602X-RAY DIFFRACTION99.64
2.34-2.520.32821370.20672606X-RAY DIFFRACTION99.71
2.52-2.770.22781370.19732587X-RAY DIFFRACTION99.63
2.77-3.170.24331370.18662613X-RAY DIFFRACTION99.53
3.17-40.20531360.1622591X-RAY DIFFRACTION98.16
4-30.190.18661390.16672618X-RAY DIFFRACTION99.14

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