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- PDB-4bgq: Crystal structure of the human CDKL5 kinase domain -

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Basic information

Entry
Database: PDB / ID: 4bgq
TitleCrystal structure of the human CDKL5 kinase domain
ComponentsCYCLIN-DEPENDENT KINASE-LIKE 5
KeywordsTRANSFERASE / PHOSPHO-MIMETIC / KINASE
Function / homology
Function and homology information


regulation of dendrite development / regulation of cilium assembly / ciliary tip / positive regulation of dendrite morphogenesis / regulation of postsynapse organization / positive regulation of dendritic spine development / positive regulation of Rac protein signal transduction / dendritic growth cone / postsynaptic density, intracellular component / positive regulation of axon extension ...regulation of dendrite development / regulation of cilium assembly / ciliary tip / positive regulation of dendrite morphogenesis / regulation of postsynapse organization / positive regulation of dendritic spine development / positive regulation of Rac protein signal transduction / dendritic growth cone / postsynaptic density, intracellular component / positive regulation of axon extension / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / dendrite cytoplasm / modulation of chemical synaptic transmission / small GTPase binding / neuron migration / kinase activity / protein kinase activity / ciliary basal body / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-38R / ACETATE ION / Cyclin-dependent kinase-like 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCanning, P. / Krojer, T. / Goubin, S. / Mahajan, P. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: Cell Rep / Year: 2018
Title: CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function.
Authors: Canning, P. / Park, K. / Goncalves, J. / Li, C. / Howard, C.J. / Sharpe, T.D. / Holt, L.J. / Pelletier, L. / Bullock, A.N. / Leroux, M.R.
History
DepositionMar 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Mar 30, 2022Group: Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_status / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE-LIKE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8567
Polymers35,2321
Non-polymers6256
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.942, 65.507, 102.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYCLIN-DEPENDENT KINASE-LIKE 5 / SERINE/THREONINE-PROTEIN KINASE 9


Mass: 35231.711 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-303 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SITE-DIRECTED MUTAGENESIS / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O76039, cyclin-dependent kinase

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Non-polymers , 5 types, 158 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-38R / [4-({4-[(3-cyclopentyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile


Mass: 359.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTWO PHOSPHOMIMETIC MUTATIONS INTRODUCED, T169D AND Y171E

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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: 2.49 Å3/Da / Density % sol: 50.59 % / Description: NONE
Crystal growDetails: 15% PEG SMEAR MEDIUM, 0.1M TRIS PH 8.0, 0.075M SODIUM ACETATE, 0.15M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→55.02 Å / Num. obs: 23993 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.8 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BBM

4bbm


Resolution: 2→55.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.306 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20135 1243 5.1 %RANDOM
Rwork0.17382 ---
obs0.17517 23136 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.581 Å2
Baniso -1Baniso -2Baniso -3
1--14.7 Å20 Å20 Å2
2--4.05 Å20 Å2
3---10.65 Å2
Refinement stepCycle: LAST / Resolution: 2→55.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 44 152 2392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192313
X-RAY DIFFRACTIONr_bond_other_d0.0010.022252
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9953129
X-RAY DIFFRACTIONr_angle_other_deg0.78835170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52623.9100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14615405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3151513
X-RAY DIFFRACTIONr_chiral_restr0.080.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
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_it1.6312.3911111
X-RAY DIFFRACTIONr_mcbond_other1.6152.3861108
X-RAY DIFFRACTIONr_mcangle_it2.7133.5571383
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8812.6061202
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 93 -
Rwork0.227 1660 -
obs--99.83 %
Refinement TLS params.

Method: refined / 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)
11.8472-2.9578-0.49844.85371.15531.5186-0.1341-0.1220.33080.14140.2152-0.5528-0.1696-0.0605-0.08120.0715-0.01820.00080.0762-0.05860.082158.034630.480948.0009
21.1191-0.1657-0.50940.02740.070.242-0.010.0078-0.0227-0.0046-0.0052-0.00160.0126-0.00120.01520.0150.0010.01020.0212-0.01170.016547.3426.78461.8775
30.2595-0.2123-0.0580.84790.62350.51670.01510.0120.0336-0.02640.0442-0.087-0.02290.0224-0.05930.02380.00220.01230.0404-0.00260.015733.523438.63871.7383
40.1908-0.1611-0.00240.56290.29930.2997-0.0162-0.0519-0.0120.0150.0195-0.00580.0287-0.0476-0.00330.0094-0.00550.00530.02750.0010.027327.794932.337872.3032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 47
2X-RAY DIFFRACTION2A52 - 162
3X-RAY DIFFRACTION3A163 - 237
4X-RAY DIFFRACTION4A238 - 302

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