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- PDB-29jc: Crystal structure of Coxsackievirus A16 (G-10) 2A protease determ... -

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Basic information

Entry
Database: PDB / ID: 29jc
TitleCrystal structure of Coxsackievirus A16 (G-10) 2A protease determined via sulfur phasing
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / Enterovirus / Coxsackievirus A16 (G-10) / 2A protease / Diamond Light Source / Beamline i23 / sulfur phasing / long wavelength / OpenBind Consortium
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 / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity ...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 / ribonucleoside triphosphate phosphatase activity / 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 / proteolysis / RNA binding / zinc ion binding / ATP binding
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 / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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 speciesCoxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsCooper, M.R. / Duman, R. / Balcomb, B.H. / Chinn, C.A. / Ebrahim, A. / Keates, T. / Marples, P.G. / V.Chandran, A. / Wang, S. / Williams, E. ...Cooper, M.R. / Duman, R. / Balcomb, B.H. / Chinn, C.A. / Ebrahim, A. / Keates, T. / Marples, P.G. / V.Chandran, A. / Wang, S. / Williams, E. / Koekemoer, L. / Fairhead, M. / Wagner, A. / Shotton, E.J. / Aschenbrenner, J.C. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other governmentG2-SCH-2025-06-16537 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of Coxsackievirus A16 (G-10) 2A protease determined via sulfur phasing
Authors: Cooper, M.R. / Duman, R. / Balcomb, B.H. / Chinn, C.A. / Ebrahim, A. / Keates, T. / Marples, P.G. / V.Chandran, A. / Wang, S. / Williams, E. / Koekemoer, L. / Fairhead, M. / Wagner, A. / ...Authors: Cooper, M.R. / Duman, R. / Balcomb, B.H. / Chinn, C.A. / Ebrahim, A. / Keates, T. / Marples, P.G. / V.Chandran, A. / Wang, S. / Williams, E. / Koekemoer, L. / Fairhead, M. / Wagner, A. / Shotton, E.J. / Aschenbrenner, J.C. / von Delft, F.
History
DepositionMar 16, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1006
Polymers31,7852
Non-polymers3154
Water6,521362
1
A: Genome polyprotein
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: Genome polyprotein
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)86.028, 56.773, 64.432
Angle α, β, γ (deg.)90, 94.95, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Genome polyprotein


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 BL21 (bacteria) / References: UniProt: Q65900
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 0.1 M MES, pH 6.7, 13%-19% w/v PEG 20,000

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jan 21, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 1.8→64.19 Å / Num. obs: 28519 / % possible obs: 99.07 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.017 / Rrim(I) all: 0.073 / Net I/σ(I): 31
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4394 / CC1/2: 0.941 / Rpim(I) all: 0.107 / Rrim(I) all: 0.218 / % possible all: 86.98

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
xia2.multiplexdata reduction
DIALS3.26.0.2data scaling
CRANK2phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.801→64.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.119 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.101
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 1922 -RANDOM
Rwork0.1606 26597 --
obs0.1624 28519 99.1 %-
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.1618 Å20 Å2-3.1949 Å2
2--1.2767 Å20 Å2
3---0.8851 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.801→64.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 14 362 2552
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092255HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.913066HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d748SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes391HARMONIC5
X-RAY DIFFRACTIONt_it2255HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2245SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.02
X-RAY DIFFRACTIONt_other_torsion15.09
LS refinement shellResolution: 1.801→1.82 Å
RfactorNum. reflection% reflection
Rfree0.1857 37 -
Rwork0.1735 534 -
obs--84.68 %
Refinement TLS params.

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)
10.3678-0.1114-0.05080.7077-0.00690.14240.0020.01690.09170.01530.04630.02870.05180.027-0.0484-0.02540.0060.0019-0.01410.02220.011722.7841.42249.7252
20.72090.4782-0.26780.5254-0.10030.4147-0.02180.02770.06830.00960.0329-0.00830.0288-0.0483-0.0111-0.02120.00650.0017-0.0177-0.00060.002212.100129.426246.2169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 141
2X-RAY DIFFRACTION1{ A|* }A201
3X-RAY DIFFRACTION2{ B|* }B1 - 141
4X-RAY DIFFRACTION2{ B|* }B201

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