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- PDB-1h4l: Structure and regulation of the CDK5-p25(nck5a) complex -

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Basic information

Entry
Database: PDB / ID: 1h4l
TitleStructure and regulation of the CDK5-p25(nck5a) complex
Components
  • CELL DIVISION PROTEIN KINASE 5
  • CYCLIN-DEPENDENT KINASE 5 ACTIVATOR
KeywordsKINASE/KINASE ACTIVATOR / KINASE-KINASE ACTIVATOR COMPLEX / COMPLEX(CYCLINS-CDK) / CYCLINS / CYCLIN-DEPENDENT KINASES / CDK5 / P35 / P25 / TRANSFERASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / PHOSPHORYLATION
Function / homology
Function and homology information


positive regulation of presynaptic cytosolic calcium concentration / negative regulation of calcium ion-dependent exocytosis of neurotransmitter / superior olivary nucleus maturation / acetylcholine receptor activator activity / protein kinase 5 complex / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / regulation of cell cycle phase transition ...positive regulation of presynaptic cytosolic calcium concentration / negative regulation of calcium ion-dependent exocytosis of neurotransmitter / superior olivary nucleus maturation / acetylcholine receptor activator activity / protein kinase 5 complex / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / regulation of cell cycle phase transition / Activated NTRK2 signals through CDK5 / negative regulation of axon extension / layer formation in cerebral cortex / neuron cell-cell adhesion / positive regulation of calcium ion-dependent exocytosis / corpus callosum development / receptor catabolic process / cerebellar cortex formation / protein localization to synapse / CRMPs in Sema3A signaling / regulation of dendritic spine morphogenesis / NGF-stimulated transcription / ErbB-3 class receptor binding / synaptic transmission, dopaminergic / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of protein export from nucleus / motor neuron axon guidance / cyclin-dependent protein serine/threonine kinase activator activity / axonal fasciculation / axon extension / calcium ion import / regulation of neuron differentiation / regulation of synaptic vesicle recycling / tau-protein kinase activity / dendrite morphogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / synaptic vesicle transport / receptor clustering / central nervous system neuron development / negative regulation of cell cycle / oligodendrocyte differentiation / peptidyl-threonine phosphorylation / synaptic vesicle exocytosis / DARPP-32 events / protein kinase activator activity / positive regulation of protein targeting to membrane / synaptic vesicle endocytosis / regulation of macroautophagy / ephrin receptor signaling pathway / cyclin-dependent protein serine/threonine kinase activity / alpha-tubulin binding / Schwann cell development / beta-tubulin binding / regulation of synaptic transmission, glutamatergic / regulation of protein localization to plasma membrane / skeletal muscle tissue development / cyclin-dependent protein kinase holoenzyme complex / synapse assembly / behavioral response to cocaine / NPAS4 regulates expression of target genes / negative regulation of proteolysis / positive regulation of microtubule polymerization / negative regulation of protein ubiquitination / ionotropic glutamate receptor binding / sensory perception of pain / ionotropic glutamate receptor signaling pathway / axonogenesis / axon guidance / regulation of cell migration / cerebellum development / cell-matrix adhesion / protein serine/threonine kinase activator activity / regulation of actin cytoskeleton organization / excitatory postsynaptic potential / synaptic transmission, glutamatergic / hippocampus development / filopodium / neuromuscular junction / intracellular protein transport / Hsp90 protein binding / brain development / peptidyl-serine phosphorylation / regulation of synaptic plasticity / visual learning / microtubule cytoskeleton organization / tau protein binding / neuron migration / G protein-coupled acetylcholine receptor signaling pathway / cellular response to amyloid-beta / neuron differentiation / neuron projection development / actin filament binding / p53 binding / kinase activity / cell junction / rhythmic process / positive regulation of neuron apoptotic process / presynapse / lamellipodium / Factors involved in megakaryocyte development and platelet production
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
Cyclin-dependent kinase 5 / Cyclin-dependent kinase 5 activator 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsTarricone, C. / Dhavan, R. / Peng, J. / Areces, L.B. / Tsai, L.-H. / Musacchio, A.
CitationJournal: Mol.Cell / Year: 2001
Title: Structure and Regulation of the Cdk5-P25(Nck5A) Complex
Authors: Tarricone, C. / Dhavan, R. / Peng, J. / Areces, L.B. / Tsai, L.-H. / Musacchio, A.
History
DepositionMay 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 8, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / diffrn_source ...atom_site / diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method ..._diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
B: CELL DIVISION PROTEIN KINASE 5
D: CYCLIN-DEPENDENT KINASE 5 ACTIVATOR
E: CYCLIN-DEPENDENT KINASE 5 ACTIVATOR


Theoretical massNumber of molelcules
Total (without water)100,7644
Polymers100,7644
Non-polymers00
Water1,24369
1
A: CELL DIVISION PROTEIN KINASE 5
D: CYCLIN-DEPENDENT KINASE 5 ACTIVATOR


Theoretical massNumber of molelcules
Total (without water)50,3822
Polymers50,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELL DIVISION PROTEIN KINASE 5
E: CYCLIN-DEPENDENT KINASE 5 ACTIVATOR


Theoretical massNumber of molelcules
Total (without water)50,3822
Polymers50,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)149.090, 89.760, 82.570
Angle α, β, γ (deg.)90.00, 93.08, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99376, 0.01698, 0.11021), (0.01563, -0.99979, 0.01308), (0.11041, -0.01128, -0.99382)
Vector: -1.77662, -28.69763, 36.80953)

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 5 / TAU PROTEIN KINASE II CATALYTIC SUBUNIT / CDK5


Mass: 33364.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PBAC4X-1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q00535
#2: Protein CYCLIN-DEPENDENT KINASE 5 ACTIVATOR / CDK5 ACTIVATOR 1 / CYCLIN-DEPENDENT KINASE 5 REGULATORY SUBUNIT 1 / TAU PROTEIN KINASE II 23 KDA ...CDK5 ACTIVATOR 1 / CYCLIN-DEPENDENT KINASE 5 REGULATORY SUBUNIT 1 / TAU PROTEIN KINASE II 23 KDA SUBUNIT / TPKII REGULATORY SUBUNIT / P23 / P25 / P35


Mass: 17017.645 Da / Num. of mol.: 2 / Fragment: RESIDUES 147-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PBAC4X-1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q15078
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG33501reservoir
2200 mM1reservoirNaI
37 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0079
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0079 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 32449 / % possible obs: 94 % / Redundancy: 2.26 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16
Reflection shellResolution: 2.65→2.74 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.6 / % possible all: 78.5
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 93.9 % / Num. measured all: 67318
Reflection shell
*PLUS
% possible obs: 78.5 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FIN

1fin


Resolution: 2.65→19.22 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1578110.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1506 5 %RANDOM
Rwork0.236 ---
obs0.236 30224 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2707 Å2 / ksol: 0.324771 e/Å3
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å22.8 Å2
2---7.23 Å20 Å2
3---4.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6868 0 0 69 6937
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 233 4.6 %
Rwork0.351 4814 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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