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- PDB-9f81: Crystal structure of RIOK2 with a covalent compound GCL 47 -

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Basic information

Entry
Database: PDB / ID: 9f81
TitleCrystal structure of RIOK2 with a covalent compound GCL 47
ComponentsSerine/threonine-protein kinase RIO2
KeywordsTRANSFERASE / Kinase / Covalent / inhibitor / RIOK2
Function / homology
Function and homology information


positive regulation of ribosomal small subunit export from nucleus / positive regulation of rRNA processing / regulation of mitotic metaphase/anaphase transition / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / ribosomal small subunit biogenesis / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity ...positive regulation of ribosomal small subunit export from nucleus / positive regulation of rRNA processing / regulation of mitotic metaphase/anaphase transition / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / ribosomal small subunit biogenesis / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Rio2 / RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / : / RIO domain / Winged helix DNA-binding domain superfamily ...Serine/threonine-protein kinase Rio2 / RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / : / RIO domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Serine/threonine-protein kinase RIO2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsWang, G.Q. / Wydra, V. / Gehringer, M. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
Citation
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2018
Title: The Cysteinome of Protein Kinases as a Target in Drug Development.
Authors: Chaikuad, A. / Koch, P. / Laufer, S.A. / Knapp, S.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase RIO2
G: Serine/threonine-protein kinase RIO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0844
Polymers76,5302
Non-polymers5552
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-8 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.177, 65.177, 180.349
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Serine/threonine-protein kinase RIO2 / RIO kinase 2


Mass: 38264.785 Da / Num. of mol.: 2 / Mutation: H149Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIOK2, RIO2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9BVS4, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1IBA / N-(4-quinazolin-4-ylphenyl)propanamide


Mass: 277.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG8000, 0.2M magnesium acetate, 0.1M cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.02→47.89 Å / Num. obs: 16922 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC1/2: 0.998 / Net I/σ(I): 11.3
Reflection shellResolution: 3.02→3.2 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2723 / CC1/2: 0.578 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→47.89 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.889 / SU B: 23.306 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 671 4 %RANDOM
Rwork0.21411 ---
obs0.2167 16212 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.794 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å21 Å2-0 Å2
2--2.01 Å2-0 Å2
3----6.52 Å2
Refinement stepCycle: 1 / Resolution: 3.02→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 42 4 4484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124580
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164297
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.8386184
X-RAY DIFFRACTIONr_angle_other_deg0.511.7679892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.895547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.6726.66736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.410803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025342
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021066
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_it8.1588.6392206
X-RAY DIFFRACTIONr_mcbond_other8.1568.642207
X-RAY DIFFRACTIONr_mcangle_it12.35815.4942747
X-RAY DIFFRACTIONr_mcangle_other12.35615.4952748
X-RAY DIFFRACTIONr_scbond_it8.989.3622374
X-RAY DIFFRACTIONr_scbond_other8.9789.3612375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.86516.93438
X-RAY DIFFRACTIONr_long_range_B_refined19.987105.8919289
X-RAY DIFFRACTIONr_long_range_B_other19.987105.8919290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.02→3.094 Å
RfactorNum. reflection% reflection
Rfree0.46 38 -
Rwork0.358 1224 -
obs--97.68 %

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