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

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Basic information

Entry
Database: PDB / ID: 7gpr
TitlePanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3C Protease in complex with POB0095
ComponentsProtease 3CPicornain 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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / protein sequestering activity / 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 / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / protein sequestering activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / : / symbiont-mediated suppression of host toll-like receptor signaling pathway / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / 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
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) / Picornavirales 3C/3C-like protease domain ...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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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
Chem-U1I / Genome polyprotein
Similarity search - Component
Biological speciesHuman Enterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)1U19AI171399 United States
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: 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.
History
DepositionAug 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: 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)40,5494
Polymers40,2522
Non-polymers2972
Water5,621312
1
A: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3452
Polymers20,1261
Non-polymers2191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2042
Polymers20,1261
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.726, 62.417, 148.217
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 / 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-U1I / methyl (3R)-3-(4-methylphenyl)pyrrolidine-3-carboxylate


Mass: 219.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.9 %
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 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.65→38.74 Å / Num. obs: 48702 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.066 / Rrim(I) all: 0.241 / Χ2: 0.41 / Net I/σ(I): 11.1 / Num. measured all: 653482
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 96.4 % / Redundancy: 13.8 % / Rmerge(I) obs: 5.68 / Num. measured all: 31517 / Num. unique obs: 2286 / CC1/2: 0.299 / Rpim(I) all: 1.592 / Rrim(I) all: 5.902 / Χ2: 0.12 / 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: 1.65→38.77 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.935 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22121 2419 5 %RANDOM
Rwork0.18362 ---
obs0.18545 45603 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å2-0 Å2
2---0.05 Å20 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.65→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 20 312 3140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133708
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153152
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.6434619
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5957261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1455450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29821.628172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6715544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6471523
X-RAY DIFFRACTIONr_chiral_restr0.0740.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024106
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02832
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_it2.1542.4841901
X-RAY DIFFRACTIONr_mcbond_other2.1712.4251853
X-RAY DIFFRACTIONr_mcangle_it3.3123.6342188
X-RAY DIFFRACTIONr_mcangle_other3.3143.6352189
X-RAY DIFFRACTIONr_scbond_it3.0852.8611807
X-RAY DIFFRACTIONr_scbond_other3.0842.8631808
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9864.152432
X-RAY DIFFRACTIONr_long_range_B_refined7.16730.3463649
X-RAY DIFFRACTIONr_long_range_B_other7.07829.6873563
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 173 -
Rwork0.33 3022 -
obs--90.92 %

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