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- PDB-29hm: Crystal structure of Enterovirus D68 3C protease determined via s... -

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Basic information

Entry
Database: PDB / ID: 29hm
TitleCrystal structure of Enterovirus D68 3C protease determined via sulfur phasing
ComponentsProtease 3C
KeywordsVIRAL PROTEIN / Enterovirus D68 / 3C protease / Diamond Light Source / Beamline i23 / sulfur phasing / long wavelength / OpenBind Consortium
Function / homology
Function and homology information


symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / 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 / protein sequestering activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity ...symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / 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 / protein sequestering activity / 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 toll-like receptor signaling pathway / symbiont-mediated suppression of host NF-kappaB cascade / 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 / cytoplasm
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 speciesenterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsChinn, C.A. / Duman, R. / Ebrahim, A. / Marples, P.G. / Cooper, M.R. / Keates, T. / V.Chandran, A. / Wang, S. / Williams, E. / Koekemoer, L. ...Chinn, C.A. / Duman, R. / Ebrahim, A. / Marples, P.G. / Cooper, M.R. / Keates, T. / 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 Enterovirus D68 3C protease determined via sulfur phasing
Authors: Chinn, C.A. / Duman, R. / Ebrahim, A. / Marples, P.G. / Cooper, M.R. / Keates, T. / V.Chandran, A. / Wang, S. / Williams, E. / Koekemoer, L. / Fairhead, M. / Wagner, A. / Shotton, E.J. / ...Authors: Chinn, C.A. / Duman, R. / Ebrahim, A. / Marples, P.G. / Cooper, M.R. / Keates, T. / V.Chandran, A. / Wang, S. / Williams, E. / Koekemoer, L. / Fairhead, M. / Wagner, A. / Shotton, E.J. / Aschenbrenner, J.C. / von Delft, F.
History
DepositionMar 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 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: Protease 3C
B: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5314
Polymers40,4602
Non-polymers712
Water4,306239
1
A: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2652
Polymers20,2301
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2652
Polymers20,2301
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.468, 104.468, 43.029
Angle α, β, γ (deg.)90, 109.27, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protease 3C / Picornain 3C / P3C


Mass: 20229.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) enterovirus D68 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q68T42, picornain 3C
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M Tris pH 7.8, 0.2 M Ammonium acetate, 50 % w/v PEG 3350

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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 28, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 1.8→104.47 Å / Num. obs: 30078 / % possible obs: 98.92 % / Redundancy: 18.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.016 / Rrim(I) all: 0.077 / Net I/σ(I): 19.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5641 / CC1/2: 0.586 / Rpim(I) all: 0.293 / Rrim(I) all: 0.649 / % possible all: 85.53

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.801→52.23 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1918 -RANDOM
Rwork0.1894 28131 --
obs0.1922 30049 98.8 %-
Displacement parametersBiso mean: 37.66 Å2
Baniso -1Baniso -2Baniso -3
1-5.4899 Å20 Å26.3372 Å2
2---0.9298 Å20 Å2
3----4.5601 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 1.801→52.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 2 239 3045
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092880HARMONIC2
X-RAY DIFFRACTIONt_angle_deg13909HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d979SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes494HARMONIC5
X-RAY DIFFRACTIONt_it2880HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion385SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2501SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.94
X-RAY DIFFRACTIONt_other_torsion15.89
LS refinement shellResolution: 1.801→1.82 Å
RfactorNum. reflection% reflection
Rfree0.4486 38 -
Rwork0.3742 563 -
obs--81.73 %
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)
11.3143-0.87860.51680.9068-0.77510.8914-0.0649-0.03120.0188-0.02110.02170.00440.00410.03340.0432-0.00930.01860.0113-0.01540.0039-0.0472-4.567961.014718.8559
20.6750.35620.25041.3296-0.66750.66120.12320.0155-0.0466-0.03150.01770.0040.02670.0037-0.14080.00820.006-0.0347-0.0797-0.01140.01582.572236.693240.4683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 182
2X-RAY DIFFRACTION2{ B|* }B2 - 181

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