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- PDB-1wmh: Crystal structure of a PB1 domain complex of Protein kinase c iot... -

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Basic information

Entry
Database: PDB / ID: 1wmh
TitleCrystal structure of a PB1 domain complex of Protein kinase c iota and Par6 alpha
Components
  • Partitioning defective-6 homolog alpha
  • Protein kinase C, iota type
KeywordsTransferase/CELL CYCLE / KINASE / PB1 DOMAIN / OPCA MOTIF / aPKC / Par6 / cell polarity / Transferase-CELL CYCLE COMPLEX
Function / homology
Function and homology information


regulation of cellular localization / Golgi vesicle budding / PAR polarity complex / Tight junction interactions / cell-cell junction maintenance / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / establishment of apical/basal cell polarity ...regulation of cellular localization / Golgi vesicle budding / PAR polarity complex / Tight junction interactions / cell-cell junction maintenance / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / establishment of apical/basal cell polarity / negative regulation of glial cell apoptotic process / eye photoreceptor cell development / GTP-dependent protein binding / positive regulation of protein localization to centrosome / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / cellular response to chemical stress / membrane organization / cell-cell junction organization / tight junction / centrosome cycle / protein targeting to membrane / RHOV GTPase cycle / positive regulation of Notch signaling pathway / establishment of cell polarity / establishment or maintenance of cell polarity / cell leading edge / brush border / RHOU GTPase cycle / CDC42 GTPase cycle / positive regulation of endothelial cell apoptotic process / bicellular tight junction / viral process / regulation of postsynaptic membrane neurotransmitter receptor levels / intercellular bridge / vesicle-mediated transport / ruffle / positive regulation of glial cell proliferation / cytoskeleton organization / RAC1 GTPase cycle / response to interleukin-1 / p75NTR recruits signalling complexes / secretion / actin filament organization / protein localization to plasma membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / positive regulation of protein secretion / positive regulation of D-glucose import / Asymmetric localization of PCP proteins / positive regulation of protein localization to plasma membrane / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / small GTPase binding / phospholipid binding / Pre-NOTCH Transcription and Translation / centriolar satellite / cellular response to insulin stimulus / positive regulation of NF-kappaB transcription factor activity / KEAP1-NFE2L2 pathway / cell migration / microtubule cytoskeleton / cell cortex / negative regulation of neuron apoptotic process / protein kinase activity / endosome / intracellular signal transduction / cilium / protein phosphorylation / apical plasma membrane / Golgi membrane / cell division / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / centrosome / negative regulation of apoptotic process / glutamatergic synapse / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Partitioning defective protein 6, PB1 domain / : / Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. ...Partitioning defective protein 6, PB1 domain / : / Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / 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 / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Protein kinase C iota type / Partitioning defective 6 homolog alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsHirano, Y. / Yoshinaga, S. / Suzuki, N.N. / Horiuchi, M. / Kohjima, M. / Takeya, R. / Sumimoto, H. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure of a Cell Polarity Regulator, a Complex between Atypical PKC and Par6 PB1 Domains
Authors: Hirano, Y. / Yoshinaga, S. / Takeya, R. / Suzuki, N.N. / Horiuchi, M. / Kohjima, M. / Sumimoto, H. / Inagaki, F.
History
DepositionJul 9, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 13, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C, iota type
B: Partitioning defective-6 homolog alpha


Theoretical massNumber of molelcules
Total (without water)19,8812
Polymers19,8812
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.150, 38.363, 45.478
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein kinase C, iota type / nPKC-iota / Atypical protein kinase C-lambda/iota / aPKC-lambda/iota


Mass: 10321.621 Da / Num. of mol.: 1 / Fragment: PB1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKCiota / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41743, EC: 2.7.1.37
#2: Protein Partitioning defective-6 homolog alpha / PAR-6 alpha / PAR-6A / PAR-6 / PAR6C / Tax interaction protein 40 / TIP-40


Mass: 9559.005 Da / Num. of mol.: 1 / Fragment: PB1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Par6alpha / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NPB6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: sodium formate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791, 0.9793, 0.9795, 0.9843
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2003 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.97951
40.98431
ReflectionResolution: 1.5→50 Å / Num. all: 50330 / Num. obs: 50330 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.206 / Num. unique all: 5073 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→35.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 724667.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2612 9.9 %RANDOM
Rwork0.216 ---
obs0.216 26353 96.9 %-
all-26353 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7209 Å2 / ksol: 0.425703 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å20 Å2
2---2.75 Å20 Å2
3----1.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 0 188 1511
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 431 10.3 %
Rwork0.242 3773 -
obs-5073 94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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