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- PDB-4fkd: Identification of the Activator Binding Residues in the Second Cy... -

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Basic information

Entry
Database: PDB / ID: 4fkd
TitleIdentification of the Activator Binding Residues in the Second Cysteine-Rich Regulatory Domain of Protein Kinase C Theta
ComponentsProtein kinase C theta type
KeywordsTRANSFERASE / PKC theta / second cysteine rich regulatory domain / activator binding site / zinc finger / Kinase
Function / homology
Function and homology information


Netrin-1 signaling / positive regulation of T-helper 2 cell activation / Apoptotic cleavage of cellular proteins / Effects of PIP2 hydrolysis / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / FCERI mediated NF-kB activation / diacylglycerol-dependent serine/threonine kinase activity / Downstream TCR signaling / regulation of platelet aggregation ...Netrin-1 signaling / positive regulation of T-helper 2 cell activation / Apoptotic cleavage of cellular proteins / Effects of PIP2 hydrolysis / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / FCERI mediated NF-kB activation / diacylglycerol-dependent serine/threonine kinase activity / Downstream TCR signaling / regulation of platelet aggregation / negative regulation of T cell apoptotic process / positive regulation of T-helper 17 type immune response / aggresome / positive regulation of filopodium assembly / immune system process / positive regulation of interleukin-17 production / positive regulation of telomere capping / membrane protein ectodomain proteolysis / immunological synapse / centriolar satellite / positive regulation of interleukin-4 production / negative regulation of insulin receptor signaling pathway / positive regulation of stress fiber assembly / positive regulation of telomerase activity / positive regulation of T cell proliferation / positive regulation of telomere maintenance via telomerase / positive regulation of interleukin-2 production / regulation of G2/M transition of mitotic cell cycle / cell chemotaxis / positive regulation of protein secretion / sarcolemma / neuromuscular junction / positive regulation of protein import into nucleus / positive regulation of T cell activation / positive regulation of NF-kappaB transcription factor activity / peptidyl-serine phosphorylation / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine/threonine kinase activity / regulation of DNA-templated transcription / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein kinase C, theta / Novel protein kinase C theta, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. ...Protein kinase C, theta / Novel protein kinase C theta, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / C2 domain profile. / 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 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / 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 / Alpha Beta
Similarity search - Domain/homology
Protein kinase C theta type
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.633 Å
AuthorsRahman, G.M. / Shanker, S. / Lewin, N.E. / Prasad, B.V.V. / Blumberg, P.M. / Das, J.
CitationJournal: Biochem.J. / Year: 2013
Title: Identification of the Activator Binding Residues in the Second Cysteine-Rich Regulatory Domain of Protein Kinase C Theta.
Authors: Rahman, G.M. / Shanker, S. / Lewin, N.E. / Kedei, N. / Hill, C.S. / Prasad, B.V. / Blumberg, P.M. / Das, J.
History
DepositionJun 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
A: Protein kinase C theta type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4463
Polymers7,3151
Non-polymers1312
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.850, 65.850, 27.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein kinase C theta type / nPKC-theta


Mass: 7315.454 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcq, Pkcq / Production host: Escherichia coli (E. coli) / References: UniProt: Q02111, protein kinase C
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M Lithium acetate and 20% PEG 3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.63→28.514 Å / Num. obs: 7559 / % possible obs: 88.39 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.63→1.72 Å / Rmerge(I) obs: 0.115 / % possible all: 98

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERMRphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.633→28.514 Å / SU ML: 0.17 / σ(F): 1.38 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 332 4.4 %Random
Rwork0.1714 ---
all0.1729 ---
obs0.1729 7550 88.39 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.887 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1944 Å20 Å20 Å2
2---3.1944 Å20 Å2
3---6.3887 Å2
Refinement stepCycle: LAST / Resolution: 1.633→28.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms509 0 2 130 641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01532
X-RAY DIFFRACTIONf_angle_d1.03705
X-RAY DIFFRACTIONf_dihedral_angle_d11.493187
X-RAY DIFFRACTIONf_chiral_restr0.06874
X-RAY DIFFRACTIONf_plane_restr0.00490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6333-2.05760.2491700.20673586X-RAY DIFFRACTION89
2.0576-28.51820.18491620.1583632X-RAY DIFFRACTION88
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)
10.83590.1154-0.07670.1626-0.04870.04340.1507-0.19690.10320.0498-0.00750.0352-0.0377-0.067-0.03670.1266-0.0228-0.0150.123-0.02140.112714.347-6.913.9808
20.17110.02280.02070.16170.06740.1016-0.0633-0.16280.01360.01180.0383-0.1359-0.0801-0.02150.0130.0893-0.0087-0.00570.08980.01930.120510.2937-26.7518-0.0817
30.2160.0840.04610.3198-0.03160.1339-0.0595-0.0032-0.076-0.00360.0319-0.0813-0.0092-0.0096-0.00520.0719-0.007-0.00530.0721-0.00740.08255.0879-27.7143-3.1975
40.16340.17140.07290.22510.19270.3131-0.10270.03170.0924-0.07950.01820.1323-0.08150.09250.0250.1185-0.0157-0.02210.1123-0.00580.104911.2409-17.5717-3.9603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:7)
2X-RAY DIFFRACTION2chain 'A' and (resseq 8:20)
3X-RAY DIFFRACTION3chain 'A' and (resseq 21:48)
4X-RAY DIFFRACTION4chain 'A' and (resseq 49:65)

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