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Basic information

Entry
Database: PDB / ID: 7h40
TitleGroup deposition for crystallographic fragment screening of Coxsackievirus A16 (G-10) 2A protease -- Crystal structure of Coxsackievirus A16 (G-10) 2A protease in complex with Z1217131798 (A71EV2A-x0526)
ComponentsProtease 2A
KeywordsHYDROLASE / Diamond Light Source / I03 / ASAP / Coxsackievirus A16 / crystallographic fragment screening / PanDDA / Pandda2 / XChemExplorer / viral protein
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / : / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
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) / Picornavirales 3C/3C-like protease domain ...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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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
(3M)-3-(2-methyl-1H-imidazol-1-yl)pyridine / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsLithgo, R.M. / Fairhead, M. / Koekemoer, L. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Golding, M. / Godoy, A.S. / Aschenbrenner, J.C. / Marples, P.G. ...Lithgo, R.M. / Fairhead, M. / Koekemoer, L. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Golding, M. / Godoy, A.S. / Aschenbrenner, J.C. / Marples, P.G. / Ni, X. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / 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: Group deposition for crystallographic fragment screening of Coxsackievirus A16 (G-10) 2A protease
Authors: Lithgo, R.M. / Fairhead, M. / Koekemoer, L. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Golding, M. / Godoy, A.S. / Aschenbrenner, J.C. / Marples, P.G. / Ni, X. / Thompson, W. / ...Authors: Lithgo, R.M. / Fairhead, M. / Koekemoer, L. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Golding, M. / Godoy, A.S. / Aschenbrenner, J.C. / Marples, P.G. / Ni, X. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / von Delft, F.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2059
Polymers16,4931
Non-polymers7118
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-5 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.244, 56.467, 32.382
Angle α, β, γ (deg.)90.00, 94.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protease 2A / P2A / Picornain 2A / Protein 2A


Mass: 16493.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65900, picornain 2A

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Non-polymers , 5 types, 236 molecules

#2: Chemical ChemComp-YZK / (3M)-3-(2-methyl-1H-imidazol-1-yl)pyridine


Mass: 159.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H9N3 / Source: (gene. exp.) Coxsackievirus A16 / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.05 / Details: 0.1 M MES, pH 6.05, 16 % PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.94054 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94054 Å / Relative weight: 1
ReflectionResolution: 1.32→47.19 Å / Num. obs: 35927 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.048 / Rrim(I) all: 0.127 / Χ2: 0.89 / Net I/σ(I): 13.7 / Num. measured all: 249101
Reflection shellResolution: 1.32→1.34 Å / % possible obs: 97.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 3.215 / Num. measured all: 12299 / Num. unique obs: 1820 / CC1/2: 0.147 / Rpim(I) all: 1.324 / Rrim(I) all: 3.483 / Χ2: 0.41 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→47.19 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25289 1786 5 %RANDOM
Rwork0.23509 ---
obs0.236 34094 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.454 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.09 Å2
2--0.26 Å20 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.32→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 38 228 1349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0152779
X-RAY DIFFRACTIONr_bond_other_d0.0360.0151763
X-RAY DIFFRACTIONr_angle_refined_deg2.5351.6162706
X-RAY DIFFRACTIONr_angle_other_deg2.5981.5824029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4135256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59521.485101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23415277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0971512
X-RAY DIFFRACTIONr_chiral_restr0.1250.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022476
X-RAY DIFFRACTIONr_gen_planes_other0.020.02488
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.632.1011437
X-RAY DIFFRACTIONr_mcbond_other1.6392.0851421
X-RAY DIFFRACTIONr_mcangle_it2.7483.1151260
X-RAY DIFFRACTIONr_mcangle_other2.7533.1211259
X-RAY DIFFRACTIONr_scbond_it2.0152.3981339
X-RAY DIFFRACTIONr_scbond_other2.0142.3991339
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1893.4961441
X-RAY DIFFRACTIONr_long_range_B_refined7.02228.8782478
X-RAY DIFFRACTIONr_long_range_B_other7.0228.9012479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.319→1.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 115 -
Rwork0.335 2498 -
obs--96.39 %

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