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- PDB-3o0g: Crystal Structure of Cdk5:p25 in complex with an ATP analogue -

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Basic information

Entry
Database: PDB / ID: 3o0g
TitleCrystal Structure of Cdk5:p25 in complex with an ATP analogue
Components
  • Cell division protein kinase 5
  • Cyclin-dependent kinase 5 activator 1
KeywordsTRANSFERASE/TRANSFERASE ACTIVATOR / kinase / Kinase activator complex / kinase inhibitor complex / TRANSFERASE-TRANSFERASE ACTIVATOR complex
Function / homology
Function and homology information


positive regulation of presynaptic cytosolic calcium concentration / negative regulation of calcium ion-dependent exocytosis of neurotransmitter / acetylcholine receptor activator activity / protein kinase 5 complex / ErbB-2 class receptor binding / cerebral cortex radially oriented cell migration / contractile muscle fiber / Activated NTRK2 signals through CDK5 / axon extension / neuron cell-cell adhesion ...positive regulation of presynaptic cytosolic calcium concentration / negative regulation of calcium ion-dependent exocytosis of neurotransmitter / acetylcholine receptor activator activity / protein kinase 5 complex / ErbB-2 class receptor binding / cerebral cortex radially oriented cell migration / contractile muscle fiber / Activated NTRK2 signals through CDK5 / axon extension / neuron cell-cell adhesion / oligodendrocyte differentiation / axonal fasciculation / NGF-stimulated transcription / CRMPs in Sema3A signaling / signaling receptor inhibitor activity / regulation of dendritic spine morphogenesis / ErbB-3 class receptor binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK / cyclin-dependent protein serine/threonine kinase activator activity / regulation of neuron differentiation / regulation of synaptic vesicle recycling / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / tau-protein kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / peptidyl-threonine phosphorylation / regulation of cell cycle phase transition / synaptic vesicle transport / synaptic vesicle exocytosis / negative regulation of proteolysis / ephrin receptor signaling pathway / DARPP-32 events / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent protein serine/threonine kinase activity / protein kinase activator activity / neuron apoptotic process / synaptic vesicle endocytosis / alpha-tubulin binding / regulation of synaptic transmission, glutamatergic / regulation of protein localization to plasma membrane / positive regulation of microtubule polymerization / beta-tubulin binding / regulation of macroautophagy / axonogenesis / NPAS4 regulates expression of target genes / synapse assembly / ionotropic glutamate receptor binding / axon guidance / ionotropic glutamate receptor signaling pathway / protein serine/threonine kinase activator activity / regulation of actin cytoskeleton organization / brain development / filopodium / neuromuscular junction / neuron migration / regulation of synaptic plasticity / Hsp90 protein binding / peptidyl-serine phosphorylation / microtubule cytoskeleton organization / tau protein binding / neuron projection development / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / kinase activity / p53 binding / G protein-coupled acetylcholine receptor signaling pathway / actin filament binding / actin cytoskeleton organization / neuron differentiation / rhythmic process / lamellipodium / presynapse / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / growth cone / protease binding / chemical synaptic transmission / Regulation of TP53 Activity through Phosphorylation / dendritic spine / regulation of apoptotic process / perikaryon / regulation of cell cycle / protein kinase activity / non-specific serine/threonine protein kinase / postsynaptic density / neuron projection / cadherin binding / protein serine kinase activity / axon / cell division / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / neuronal cell body / calcium ion binding / dendrite / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / membrane
Similarity search - Function
Cyclin-dependent kinase 5 activator protein / Cyclin-dependent kinase 5 activator / Cyclin-like / Cyclin A; domain 1 / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Cyclin-dependent kinase 5 activator protein / Cyclin-dependent kinase 5 activator / Cyclin-like / Cyclin A; domain 1 / Cyclin-like superfamily / : / 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-3O0 / Cyclin-dependent kinase 5 / Cyclin-dependent kinase 5 activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsMapelli, M.
CitationJournal: Chem.Biol. / Year: 2005
Title: Defining Cdk5 ligand chemical space with small molecule inhibitors of Tau phosphorylation
Authors: Ahn, J.S. / Radhakrishnan, M.L. / Mapelli, M. / Choi, S. / Tidor, B. / Cuny, G.D. / Musacchio, A. / Yeh, L. / Kosik, S.K.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 5
D: Cyclin-dependent kinase 5 activator 1
B: Cell division protein kinase 5
E: Cyclin-dependent kinase 5 activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5075
Polymers101,1334
Non-polymers3751
Water4,216234
1
A: Cell division protein kinase 5
D: Cyclin-dependent kinase 5 activator 1


Theoretical massNumber of molelcules
Total (without water)50,5662
Polymers50,5662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-18 kcal/mol
Surface area19030 Å2
MethodPISA
2
B: Cell division protein kinase 5
E: Cyclin-dependent kinase 5 activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9413
Polymers50,5662
Non-polymers3751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-18 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.124, 117.124, 155.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cell division protein kinase 5 / Cyclin-dependent kinase 5 / Tau protein kinase II catalytic subunit / TPKII catalytic subunit / ...Cyclin-dependent kinase 5 / Tau protein kinase II catalytic subunit / TPKII catalytic subunit / Serine/threonine-protein kinase PSSALRE


Mass: 33349.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Cdk5 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00535, cyclin-dependent kinase
#2: Protein Cyclin-dependent kinase 5 activator 1 / CDK5 activator 1 / Cyclin-dependent kinase 5 regulatory subunit 1 / TPKII regulatory subunit / ...CDK5 activator 1 / Cyclin-dependent kinase 5 regulatory subunit 1 / TPKII regulatory subunit / Cyclin-dependent kinase 5 activator 1 / p25 / p25 / Tau protein kinase II 23 kDa subunit / p23


Mass: 17216.852 Da / Num. of mol.: 2 / Fragment: UNP residues 146-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: p25 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15078
#3: Chemical ChemComp-3O0 / {4-amino-2-[(4-chlorophenyl)amino]-1,3-thiazol-5-yl}(3-nitrophenyl)methanone


Mass: 374.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11ClN4O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 293 K / pH: 7
Details: PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 88794 / % possible obs: 98.6 % / Rsym value: 0.04 / Net I/σ(I): 17.3
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.29

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
AMoREphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H4L

1h4l


Resolution: 1.95→19.96 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.598 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25626 4474 5 %RANDOM
Rwork0.22613 ---
obs0.22763 84271 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6846 0 25 234 7105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217033
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.181.9769523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1175844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025282
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.23350
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2312
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5231.54260
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it126889
X-RAY DIFFRACTIONr_scbond_it1.65432773
X-RAY DIFFRACTIONr_scangle_it2.494.52634
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 284
Rwork0.263 5433
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)
11.1724-0.4923-0.43662.26390.73461.7777-0.0159-0.0979-0.04-0.05930.0231-0.15520.14150.1101-0.00720.00230.0017-0.01010.05590.00730.050246.828730.359633.2754
23.01631.4407-0.6262.7103-0.8553.0111-0.21520.3751-0.1418-0.28750.1363-0.16960.2433-0.04620.07890.0607-0.09580.00330.1520.00270.0789-18.057360.731269.4907
31.1738-1.32330.65844.1318-0.59691.9025-0.0473-0.1325-0.00220.18360.1190.25090.0057-0.1438-0.07160.0878-0.03310.0040.05620.03520.048348.09731.045843.271
43.5588-2.760.49588.8314-1.00234.27620.04630.0565-0.8237-0.14920.1196-0.39130.90660.6305-0.16590.6211-0.0410.10490.4852-0.13560.6763-13.335428.35368.4874
529.81464.861-14.054621.503912.862218.9353-0.35190.0911-0.7526-0.3009-0.4604-1.00750.2956-0.30710.81230.2260.00020.00620.2229-0.00260.2216-5.949660.19660.8667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 82
2X-RAY DIFFRACTION1A83 - 289
3X-RAY DIFFRACTION2B6 - 82
4X-RAY DIFFRACTION2B83 - 288
5X-RAY DIFFRACTION3D145 - 293
6X-RAY DIFFRACTION4E145 - 293
7X-RAY DIFFRACTION5M1

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