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- PDB-5ih6: Human Casein Kinase 1 isoform delta (kinase domain) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5ih6
TitleHuman Casein Kinase 1 isoform delta (kinase domain) in complex with Epiblastin A derivative
ComponentsCasein kinase I isoform delta
KeywordsTRANSFERASE / Kinase domain / stem cell reprogramming / kinase inhibitor complex
Function / homology
Function and homology information


positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / tau-protein kinase / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / protein localization to cilium / tau-protein kinase / non-motile cilium assembly / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / ciliary basal body / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
6-(3-bromophenyl)pteridine-2,4,7-triamine / S,R MESO-TARTARIC ACID / Casein kinase I isoform delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsUrsu, A. / Illich, D.J. / Takemoto, Y. / Porfetye, A.T. / Zhang, M. / Brockmeyer, A. / Janning, P. / Watanabe, N. / Osada, H. / Vetter, I.R. ...Ursu, A. / Illich, D.J. / Takemoto, Y. / Porfetye, A.T. / Zhang, M. / Brockmeyer, A. / Janning, P. / Watanabe, N. / Osada, H. / Vetter, I.R. / Ziegler, S. / Schoeler, H.R. / Waldmann, H.
CitationJournal: Cell Chem Biol / Year: 2016
Title: Epiblastin A Induces Reprogramming of Epiblast Stem Cells Into Embryonic Stem Cells by Inhibition of Casein Kinase 1.
Authors: Ursu, A. / Illich, D.J. / Takemoto, Y. / Porfetye, A.T. / Zhang, M. / Brockmeyer, A. / Janning, P. / Watanabe, N. / Osada, H. / Vetter, I.R. / Ziegler, S. / Scholer, H.R. / Waldmann, H.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase I isoform delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9466
Polymers34,2071
Non-polymers7405
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-53 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.720, 65.720, 151.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Casein kinase I isoform delta / CKId / Tau-protein kinase CSNK1D


Mass: 34206.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal cloning artifact: GP / Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase

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Non-polymers , 5 types, 27 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-AUG / 6-(3-bromophenyl)pteridine-2,4,7-triamine


Mass: 332.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10BrN7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Li2SO4, 0.7 - 0.8 M Na-K tartrate, 0.1 M CHES
PH range: 9.3-9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.76995 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.76995 Å / Relative weight: 1
ReflectionResolution: 2.3→37.8 Å / Num. obs: 17269 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 62.054 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.119 / Χ2: 1.126 / Net I/σ(I): 12.49 / Num. measured all: 243801
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.367.11.4811.077992127311310.2321.59788.8
2.36-2.421.3511.4511343126112050.4011.4395.6
2.42-2.491.3881.6814021118611440.4641.44996.5
2.49-2.571.2822.217458116411370.7911.32697.7
2.57-2.661.1142.6417387115111440.9181.15399.4
2.66-2.750.8213.6616688111811150.980.85199.7
2.75-2.850.6734.4515926107610730.9850.69799.7
2.85-2.970.5365.8816140101110090.990.55499.8
2.97-3.10.3847.63154689759740.9950.39799.9
3.1-3.250.27110.2145259569560.9950.28100
3.25-3.430.18213.69137339049030.9980.18899.9
3.43-3.640.14916.64140238688680.9980.155100
3.64-3.890.13220.21125158098080.9980.13799.9
3.89-4.20.08227.09111107497490.9990.085100
4.2-4.60.07132.87109877087080.9990.074100
4.6-5.140.06834.731015564964910.07100
5.14-5.940.07133.584275775770.9980.074100
5.94-7.270.06236.3772474894890.9990.064100
7.27-10.290.04542.7956443913910.9990.047100
10.290.04742.9630122452390.9990.04997.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH4

5ih4


Resolution: 2.3→37.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.952 / SU B: 15.112 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 864 5 %RANDOM
Rwork0.2329 ---
obs0.2344 16405 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.68 Å2 / Biso mean: 89.694 Å2 / Biso min: 35.13 Å2
Baniso -1Baniso -2Baniso -3
1-3.06 Å21.53 Å20 Å2
2--3.06 Å2-0 Å2
3----9.94 Å2
Refinement stepCycle: final / Resolution: 2.3→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 41 22 2404
Biso mean--91.95 65.6 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192440
X-RAY DIFFRACTIONr_bond_other_d0.0020.022309
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9793285
X-RAY DIFFRACTIONr_angle_other_deg0.99435297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25322.941119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83815438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9351520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022733
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02609
X-RAY DIFFRACTIONr_mcbond_it7.1518.5371144
X-RAY DIFFRACTIONr_mcbond_other7.148.5311143
X-RAY DIFFRACTIONr_mcangle_it10.45712.7631427
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 56 -
Rwork0.542 1071 -
all-1127 -
obs--88.67 %

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