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- PDB-7hzf: Group deposition of Coxsackievirus A16 (G-10) 2A protease in comp... -

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Basic information

Entry
Database: PDB / ID: 7hzf
TitleGroup deposition of Coxsackievirus A16 (G-10) 2A protease in complex with inhibitors from the ASAP AViDD centre -- Crystal structure of Coxsackievirus A16 (G-10) 2A protease in complex with ASAP-0036379-001 (A71EV2A-x4541)
ComponentsProtease 2A
KeywordsHYDROLASE / Diamond Light Source / I04-1 / ASAP / A71 2A / enterovirus / protease / 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host NF-kappaB cascade / DNA replication / 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
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
: / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.543 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. / Kenton, N. / Tucker, J. / DiPoto, M. / Lee, A. / 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 of Coxsackievirus A16 (G-10) 2A protease in complex with inhibitors from the ASAP AViDD centre
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. / Kenton, N. / Tucker, J. / DiPoto, M. / Lee, A. / Fearon, D. / von Delft, F.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: 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
C: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5646
Polymers31,7852
Non-polymers7784
Water6,864381
1
A: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2823
Polymers15,8931
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2823
Polymers15,8931
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.759, 61.736, 65.666
Angle α, β, γ (deg.)90.00, 92.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 15892.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65900, picornain 2A
#2: Chemical ChemComp-A1BN7 / (3S)-1-[(5-chloro-1,2-thiazol-4-yl)di(fluoro)acetyl]piperidine-3-carboxamide


Mass: 323.747 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12ClF2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.32 Å3/Da / Density % sol: 46.91 %
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: I04-1 / Wavelength: 0.92201 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92201 Å / Relative weight: 1
ReflectionResolution: 1.54→47.05 Å / Num. obs: 42755 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.069 / Rrim(I) all: 0.181 / Χ2: 0.89 / Net I/σ(I): 7.2 / Num. measured all: 291156
Reflection shellResolution: 1.54→1.63 Å / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.743 / Num. measured all: 36917 / Num. unique obs: 6222 / CC1/2: 0.407 / Rpim(I) all: 0.775 / Rrim(I) all: 1.913 / Χ2: 0.78 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.543→47.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.083 / SU Rfree Cruickshank DPI: 0.078
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 2109 4.94 %RANDOM
Rwork0.1825 ---
obs0.1837 42674 99.7 %-
Displacement parametersBiso mean: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.0913 Å20 Å2-0.428 Å2
2--0.879 Å20 Å2
3----0.7876 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.543→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 42 381 2571
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012250HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.983068HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d752SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes404HARMONIC5
X-RAY DIFFRACTIONt_it2250HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.25
X-RAY DIFFRACTIONt_other_torsion13.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion276SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2061SEMIHARMONIC4
LS refinement shellResolution: 1.54→1.55 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3836 37 4.33 %
Rwork0.2984 817 -
all0.302 854 -
obs--94.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4756-0.324-0.06891.0499-0.05180.3479-0.0084-00.02850.03740.01430.05420.0290.0257-0.0059-0.0192-0.00330.0113-0.02790.00190.000619.6456.743418.3679
20.47220.30870.0110.9020.09480.4138-0.02120.01720.02840.01030.0308-0.03980.001-0.0144-0.0096-0.01670.00020.0043-0.026-0.0019-0.002115.198-23.955214.1953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }

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