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- PDB-7gqa: PanDDA analysis group deposition -- Crystal Structure of Enterovi... -

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Basic information

Entry
Database: PDB / ID: 7gqa
TitlePanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with Z57299966
ComponentsProtease 3C
KeywordsVIRAL PROTEIN / Diamond I04-1 fragment screening / PanDDA / XChemExplorer / XCE / Viral Protease / 3C
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 / protein sequestering 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 ...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 / protein sequestering 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 / channel activity / symbiont-mediated suppression of host NF-kappaB cascade / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 / 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 (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
(1-methyl-1H-benzimidazol-2-yl)methanol / Genome polyprotein
Similarity search - Component
Biological speciesHuman Enterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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)U19AI171399 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
DepositionAug 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.grant_number
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Protease 3C
B: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4924
Polymers40,2522
Non-polymers2402
Water5,783321
1
A: Protease 3C


Theoretical massNumber of molelcules
Total (without water)20,1261
Polymers20,1261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3663
Polymers20,1261
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.830, 62.750, 147.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20126.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human Enterovirus D68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68T42, picornain 3C
#2: Chemical ChemComp-T1U / (1-methyl-1H-benzimidazol-2-yl)methanol


Mass: 162.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.14 / Details: 25% PEG 3350, 0.1M Tris, 0.2M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.66→38.7 Å / Num. obs: 47964 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.325 / Rpim(I) all: 0.099 / Rrim(I) all: 0.34 / Χ2: 0.97 / Net I/σ(I): 8.1 / Num. measured all: 562625
Reflection shellResolution: 1.66→1.7 Å / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 2.784 / Num. measured all: 39267 / Num. unique obs: 3483 / CC1/2: 0.366 / Rpim(I) all: 0.853 / Rrim(I) all: 2.916 / Χ2: 0.77 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→38.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.959 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 2403 5 %RANDOM
Rwork0.20043 ---
obs0.20181 45466 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.2 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.66→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 16 321 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133250
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152889
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.6414226
X-RAY DIFFRACTIONr_angle_other_deg1.3691.5896642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4435408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61721.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35715502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1121523
X-RAY DIFFRACTIONr_chiral_restr0.0750.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02757
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_it2.0042.0321663
X-RAY DIFFRACTIONr_mcbond_other2.0212.0041636
X-RAY DIFFRACTIONr_mcangle_it3.0142.981996
X-RAY DIFFRACTIONr_mcangle_other3.0132.9821997
X-RAY DIFFRACTIONr_scbond_it2.9012.4141587
X-RAY DIFFRACTIONr_scbond_other2.92.4161588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.613.4632231
X-RAY DIFFRACTIONr_long_range_B_refined6.74125.0433310
X-RAY DIFFRACTIONr_long_range_B_other6.72524.5493236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 188 -
Rwork0.374 3275 -
obs--99.45 %

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