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- PDB-2jed: The crystal structure of the kinase domain of the protein kinase ... -

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Basic information

Entry
Database: PDB / ID: 2jed
TitleThe crystal structure of the kinase domain of the protein kinase C theta in complex with NVP-XAA228 at 2.32A resolution.
ComponentsPROTEIN KINASE C THETA
KeywordsTRANSFERASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / POLYMORPHISM / METAL-BINDING / ZINC / KINASE / PKC THETA / MAGNESIUM / ZINC-FINGER / ALTERNATIVE SPLICING / PHORBOL-ESTER BINDING
Function / homology
Function and homology information


positive regulation of T-helper 2 cell activation / Netrin-1 signaling / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / regulation of platelet aggregation / Effects of PIP2 hydrolysis / CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell apoptotic process / positive regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of T-helper 17 type immune response ...positive regulation of T-helper 2 cell activation / Netrin-1 signaling / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / regulation of platelet aggregation / Effects of PIP2 hydrolysis / CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell apoptotic process / positive regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of T-helper 17 type immune response / aggresome / Apoptotic cleavage of cellular proteins / positive regulation of interleukin-4 production / Fc-epsilon receptor signaling pathway / positive regulation of telomere maintenance / positive regulation of interleukin-17 production / membrane protein ectodomain proteolysis / immunological synapse / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / axon guidance / cell chemotaxis / regulation of cell growth / positive regulation of NF-kappaB transcription factor activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of T cell activation / FCERI mediated NF-kB activation / centriolar satellite / RAS processing / G alpha (z) signalling events / Downstream TCR signaling / Inactivation, recovery and regulation of the phototransduction cascade / protein phosphorylation / protein kinase activity / intracellular signal transduction / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / zinc ion binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
Protein kinase C, theta / Novel protein kinase C theta, catalytic domain / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...Protein kinase C, theta / Novel protein kinase C theta, catalytic domain / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain 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-LG8 / Protein kinase C theta type
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsStark, W. / Bitsch, F. / Berner, A. / Buelens, F. / Graff, P. / Depersin, H. / Geiser, M. / Knecht, R. / Rahuel, J. / Rummel, G. ...Stark, W. / Bitsch, F. / Berner, A. / Buelens, F. / Graff, P. / Depersin, H. / Geiser, M. / Knecht, R. / Rahuel, J. / Rummel, G. / Schlaeppi, J.M. / Schmitz, R. / Strauss, A. / Wagner, J.
Citation
Journal: To be Published
Title: The Crystal Structure of the Kinase Domain of the Protein Kinase C Theta in Complex with Nvp-Xaa228
Authors: Stark, W. / Bitsch, F. / Berner, A. / Buelens, F. / Graff, P. / Depersin, H. / Fendrich, G. / Geiser, M. / Knecht, R. / Rahuel, J. / Rummel, G. / Schlaeppi, J.M. / Schmitz, R. / Strauss, A. / Wagner, J.
#1: Journal: Protein Expression Purif. / Year: 2007
Title: Improved Expression of Kinases in Baculovirus-Infected Insect Cells Upon Addition of Specific Kinase Inhibitors to the Culture Helpful for Structural Studies.
Authors: Strauss, A. / Fendrich, G. / Horisberger, M.A. / Liebetanz, J. / Meyhack, B. / Schlaeppi, J.-M. / Schmitz, R.
History
DepositionJan 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.5Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE C THETA
B: PROTEIN KINASE C THETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6715
Polymers83,6482
Non-polymers1,0233
Water7,422412
1
A: PROTEIN KINASE C THETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2772
Polymers41,8241
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEIN KINASE C THETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3953
Polymers41,8241
Non-polymers5712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)152.172, 152.172, 74.837
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PROTEIN KINASE C THETA / NPKC-THETA


Mass: 41823.965 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN 361-706 / Mutation: YES / Source method: isolated from a natural source
Details: PHOSPHOSERINE 676, PHOSPHOSERINE 695, C540 MODIFIED
Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q04759, protein kinase C
#2: Chemical ChemComp-LG8 / 3-(8-DIMETHYLAMINOMETHYL-6,7,8,9-TETRAHYDRO-PYRIDO[1,2-A]INDOL-10-YL)-4-(1-METHYL-1H-INDOL-3-YL)-PYRROLE-2,5-DIONE


Mass: 452.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H28N4O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 381 TO GLU ENGINEERED RESIDUE IN CHAIN A, THR 538 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, ILE 381 TO GLU ENGINEERED RESIDUE IN CHAIN A, THR 538 TO GLU ENGINEERED RESIDUE IN CHAIN B, ILE 381 TO GLU ENGINEERED RESIDUE IN CHAIN B, THR 538 TO GLU
Has protein modificationY
Sequence detailsMUTATIONS I381E, T538E

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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: 3.14 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: VAPOR DIFFUSION AT 4C PROTEIN SOLUTION: 10MG/ML PROTEIN IN 0.2M NACL, 0.05M IMIDAZOLE, 0.001M NAF, 0.05M TCEP, PH = 8.0 RESERVOIR SOLUTION: 0.1 M NA-CACODYLATE PH = 6.5 24% MPD (V/V) 4% ...Details: VAPOR DIFFUSION AT 4C PROTEIN SOLUTION: 10MG/ML PROTEIN IN 0.2M NACL, 0.05M IMIDAZOLE, 0.001M NAF, 0.05M TCEP, PH = 8.0 RESERVOIR SOLUTION: 0.1 M NA-CACODYLATE PH = 6.5 24% MPD (V/V) 4% PEG8000 (W/V) DROP: 1:1 SMALL ORGANIC MOLECULES LIKE 2,5-HEXANEDIOL AND SULFOBETAINE-195 HAVE A POSITIVE EFFECT ON THE CRYSTAL GROWTH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.918396
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918396 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 42831 / % possible obs: 99.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 2.32→2.36 Å / Rmerge(I) obs: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FOT

1fot


Resolution: 2.32→19.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.404 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2131 5 %RANDOM
Rwork0.186 ---
obs0.188 40693 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å20 Å2
2---0.17 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.32→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5396 0 76 412 5884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225624
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9747582
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1285645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7924.069290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00115.0591020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0111531
X-RAY DIFFRACTIONr_chiral_restr0.1090.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024276
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.22324
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23739
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2400
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7341.53333
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22225200
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.86132636
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8474.52382
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: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 134 -
Rwork0.247 2961 -
obs--100 %

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