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- PDB-8poa: Structure of Coxsackievirus A16 (G-10) 2A protease -

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Basic information

Entry
Database: PDB / ID: 8poa
TitleStructure of Coxsackievirus A16 (G-10) 2A protease
ComponentsProtease 2A
KeywordsVIRAL PROTEIN / Enterovirus 2A protease ASAP AViDD Cysteine / Cysteine protease / ANTIVIRAL 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
Biological speciesHuman coxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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. / Thompson, W. ...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. / Thompson, W. / 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)U19AI71399 United States
CitationJournal: Biorxiv / Year: 2024
Title: Crystallographic Fragment Screen of Coxsackievirus A16 2A Protease identifies new opportunities for the development of broad-spectrum anti-enterovirals.
Authors: Lithgo, R.M. / Tomlinson, C.W.E. / Fairhead, M. / Winokan, M. / Thompson, W. / Wild, C. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Chandran, A.V. / Golding, M. / Koekemoer, L. / ...Authors: Lithgo, R.M. / Tomlinson, C.W.E. / Fairhead, M. / Winokan, M. / Thompson, W. / Wild, C. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Chandran, A.V. / Golding, M. / Koekemoer, L. / Williams, E.P. / Wang, S. / Ni, X. / MacLean, E. / Giroud, C. / Godoy, A.S. / Xavier, M.A. / Walsh, M. / Fearon, D. / von Delft, F.
History
DepositionJul 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title
Revision 2.0Jul 3, 2024Group: Atomic model / Data collection / Source and taxonomy / Category: atom_site / entity_src_gen / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease 2A
B: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1006
Polymers31,7852
Non-polymers3154
Water6,630368
1
A: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0503
Polymers15,8931
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0503
Polymers15,8931
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.128, 57.199, 64.631
Angle α, β, γ (deg.)90.00, 95.23, 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.) Human coxsackievirus A16 (strain G-10) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q65900, picornain 2A
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium Formate 20% PEG 3350

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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: May 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 1.6→16.09 Å / Num. obs: 41210 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.18 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1461 / Rpim(I) all: 0.05993 / Rrim(I) all: 0.1581 / Net I/σ(I): 10.43
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.7042 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 4072 / CC1/2: 0.653 / CC star: 0.889 / Rpim(I) all: 0.3338 / Rrim(I) all: 0.7818 / % possible all: 98.91

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (14-JUN-2023)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→16.09 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.093 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.084
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 2015 4.89 %RANDOM
Rwork0.1858 ---
obs0.187 41210 99.6 %-
Displacement parametersBiso mean: 18.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.2811 Å20 Å2-1.2878 Å2
2---0.6548 Å20 Å2
3---0.9359 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→16.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 14 368 2548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012266HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933085HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d760SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes397HARMONIC5
X-RAY DIFFRACTIONt_it2266HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion15.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
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_contact2156SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.61 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3014 -3.88 %
Rwork0.2546 793 -
all0.2564 825 -
obs--98.45 %
Refinement TLS params.

T22: -0.0148 Å2 / 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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5730.0972-0.01120.7834-0.00520.28160.0057-0.00160.085-0.00730.038-0.03920.0372-0.0236-0.0436-0.021-0.0039-0.0018-0.0115-0.008114.54177.327114.8677
20.7806-0.2919-0.13440.4723-0.08610.42190.0035-0.02090.059-0.00990.00880.02090.02160.0307-0.0123-0.0195-0.01020.0009-0.0014-0.009525.255135.574117.895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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