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Open data
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Basic information
Entry | Database: PDB / ID: 1h4l | |||||||||
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Title | Structure and regulation of the CDK5-p25(nck5a) complex | |||||||||
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![]() | KINASE/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 | ![]() superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / neuron cell-cell adhesion ...superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / neuron cell-cell adhesion / positive regulation of calcium ion-dependent exocytosis / negative regulation of axon extension / receptor catabolic process / regulation of synaptic vesicle cycle / protein localization to synapse / corpus callosum development / regulation of dendritic spine morphogenesis / cerebellar cortex formation / CRMPs in Sema3A signaling / NGF-stimulated transcription / synaptic transmission, dopaminergic / ErbB-3 class receptor binding / calcium ion import / negative regulation of protein export from nucleus / axon extension / cyclin-dependent protein serine/threonine kinase activator activity / regulation of synaptic vesicle recycling / axonal fasciculation / motor neuron axon guidance / dendrite morphogenesis / embryo development ending in birth or egg hatching / regulation of neuron differentiation / synaptic vesicle transport / regulation of cyclin-dependent protein serine/threonine kinase activity / tau-protein kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / beta-tubulin binding / protein kinase activator activity / central nervous system neuron development / oligodendrocyte differentiation / receptor clustering / synaptic vesicle exocytosis / behavioral response to cocaine / synaptic vesicle endocytosis / negative regulation of cell cycle / DARPP-32 events / alpha-tubulin binding / cyclin-dependent protein kinase holoenzyme complex / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / regulation of protein localization to plasma membrane / regulation of macroautophagy / cyclin-dependent protein serine/threonine kinase activity / Schwann cell development / skeletal muscle tissue development / regulation of synaptic transmission, glutamatergic / regulation of cell migration / sensory perception of pain / positive regulation of microtubule polymerization / negative regulation of protein ubiquitination / synapse assembly / NPAS4 regulates expression of target genes / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / ephrin receptor binding / protein serine/threonine kinase activator activity / cerebellum development / axonogenesis / cell-matrix adhesion / filopodium / synaptic transmission, glutamatergic / hippocampus development / negative regulation of proteolysis / regulation of actin cytoskeleton organization / peptidyl-threonine phosphorylation / axon guidance / intracellular protein transport / ionotropic glutamate receptor binding / neuron migration / Hsp90 protein binding / visual learning / regulation of synaptic plasticity / tau protein binding / neuromuscular junction / neuron differentiation / G protein-coupled acetylcholine receptor signaling pathway / brain development / microtubule cytoskeleton organization / cellular response to amyloid-beta / neuron projection development / actin filament binding / positive regulation of neuron apoptotic process / rhythmic process / p53 binding / presynapse / cell junction / lamellipodium / kinase activity / Factors involved in megakaryocyte development and platelet production / growth cone Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tarricone, C. / Dhavan, R. / Peng, J. / Areces, L.B. / Tsai, L.-H. / Musacchio, A. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.3 KB | Display | ![]() |
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PDB format | ![]() | 133.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
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Full document | ![]() | 477.5 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1finS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99376, 0.01698, 0.11021), Vector: |
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Components
#1: Protein | Mass: 33364.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 17017.645 Da / Num. of mol.: 2 / Fragment: RESIDUES 147-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.07 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0079 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.2707 Å2 / ksol: 0.324771 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→19.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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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
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