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- PDB-4dc2: Structure of PKC in Complex with a Substrate Peptide from Par-3 -

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Basic information

Entry
Database: PDB / ID: 4dc2
TitleStructure of PKC in Complex with a Substrate Peptide from Par-3
Components
  • Partitioning defective 3 homolog
  • Protein kinase C iota type
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / Kinase / substrate / Cell polarity / Par-3 / atypical PKC / TRANSFERASE-TRANSFERASE SUBSTRATE complex
Function / homology
Function and homology information


Pre-NOTCH Transcription and Translation / Tight junction interactions / Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / Golgi vesicle budding / p75NTR recruits signalling complexes / PAR polarity complex ...Pre-NOTCH Transcription and Translation / Tight junction interactions / Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / Golgi vesicle budding / p75NTR recruits signalling complexes / PAR polarity complex / apical constriction / establishment of centrosome localization / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / establishment of apical/basal cell polarity / establishment of epithelial cell polarity / positive regulation of myelination / negative regulation of glial cell apoptotic process / lateral loop / eye photoreceptor cell development / bicellular tight junction assembly / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of peptidyl-threonine phosphorylation / myelination in peripheral nervous system / KEAP1-NFE2L2 pathway / cell-cell junction organization / phosphatidylinositol-3-phosphate binding / protein targeting to membrane / wound healing, spreading of cells / centrosome localization / apical junction complex / establishment of cell polarity / cell leading edge / phosphatidylinositol-3,4,5-trisphosphate binding / brush border / positive regulation of receptor internalization / positive regulation of endothelial cell apoptotic process / bicellular tight junction / regulation of postsynaptic membrane neurotransmitter receptor levels / axonal growth cone / intercellular bridge / positive regulation of glial cell proliferation / phosphatidylinositol-4,5-bisphosphate binding / endomembrane system / phosphatidylinositol binding / response to interleukin-1 / actin filament organization / positive regulation of D-glucose import / adherens junction / positive regulation of protein localization to plasma membrane / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / phospholipid binding / microtubule cytoskeleton organization / spindle / cellular response to insulin stimulus / positive regulation of NF-kappaB transcription factor activity / cell junction / apical part of cell / intracellular protein localization / cell-cell junction / cell migration / microtubule cytoskeleton / cell cortex / protein phosphatase binding / negative regulation of neuron apoptotic process / protein kinase activity / endosome / cell adhesion / cilium / apical plasma membrane / Golgi membrane / cell division / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / glutamatergic synapse / protein-containing complex / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Par3/HAL, N-terminal / Protein kinase C, PB1 domain / N-terminal of Par3 and HAL proteins / : / PB1 domain / PB1 domain / PB1 domain / : ...Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Par3/HAL, N-terminal / Protein kinase C, PB1 domain / N-terminal of Par3 and HAL proteins / : / 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. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ 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
ADENINE / Protein kinase C iota type / Partitioning defective 3 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShang, Y. / Wang, C. / Yu, J. / Zhang, M.
CitationJournal: Structure / Year: 2012
Title: Substrate recognition mechanism of atypical protein kinase Cs revealed by the structure of PKC iota in complex with a substrate peptide from Par-3
Authors: Wang, C. / Shang, Y. / Yu, J. / Zhang, M.
History
DepositionJan 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C iota type
Z: Partitioning defective 3 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0403
Polymers48,9052
Non-polymers1351
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-6 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.456, 54.900, 82.489
Angle α, β, γ (deg.)90.00, 115.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 45697.207 Da / Num. of mol.: 1 / Fragment: UNP residues 231-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pkcl / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q62074, protein kinase C
#2: Protein/peptide Partitioning defective 3 homolog / PAR-3 / PARD-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Atypical PKC-specific- ...PAR-3 / PARD-3 / Atypical PKC isotype-specific-interacting protein / ASIP / Atypical PKC-specific-binding protein / ASBP


Mass: 3207.556 Da / Num. of mol.: 1 / Fragment: Substrate Peptide, UNP residues 813-840 / Source method: obtained synthetically
Details: This sequence occurs naturally in humans/mouses/rats.
Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q9Z340
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5M sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→21.2 Å / Num. all: 16230 / Num. obs: 13400 / % possible obs: 82.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 32.72 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7_629)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→21.179 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8302 / SU ML: 0.33 / σ(F): 0 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 659 4.92 %RANDOM
Rwork0.1723 ---
all0.1757 16230 --
obs0.1757 13400 82.56 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.251 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 178.12 Å2 / Biso mean: 43.3645 Å2 / Biso min: 6.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.1692 Å2-0 Å21.2238 Å2
2--0.697 Å2-0 Å2
3---1.4722 Å2
Refinement stepCycle: LAST / Resolution: 2.4→21.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 10 52 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082764
X-RAY DIFFRACTIONf_angle_d1.1323747
X-RAY DIFFRACTIONf_chiral_restr0.078406
X-RAY DIFFRACTIONf_plane_restr0.005485
X-RAY DIFFRACTIONf_dihedral_angle_d14.204981
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.5850.2991190.21362321244076
2.585-2.84460.29821290.20482509263882
2.8446-3.2550.27231320.19042647277986
3.255-4.09610.24881300.15562651278186
4.0961-21.18030.19731490.15562613276283
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)
10.52960.38860.43060.5216-0.04530.762-0.13340.2568-0.0035-0.12770.1525-0.0873-0.19560.0688-0.03550.1875-0.04660.03480.18020.00110.12936.5796-9.711313.7984
20.24940.01050.04670.0624-0.13170.5965-0.009-0.0222-0.16270.06650.0475-0.15270.2727-0.1993-0.04730.09930.0122-0.05550.03950.00980.15092.4416-25.608827.4723
30.25850.03370.09790.36410.05810.67010.0551-0.0014-0.01010.0130.41920.1662-0.4131-0.54950.06410.0402-0.1655-0.0554-0.1354-0.2453-0.07950.0215-12.838119.0586
40.2002-0.02060.10390.62550.0760.08550.09540.0209-0.09740.09090.0117-0.25220.1370.0877-0.00240.1578-0.05110.02530.25440.01360.35179.9009-15.103731.7255
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 239:394)A239 - 394
2X-RAY DIFFRACTION2(chain A and resid 395:469)A395 - 469
3X-RAY DIFFRACTION3(chain A and resid 470:577)A470 - 577
4X-RAY DIFFRACTION4(chain Z and resid 1047:1062)Z1047 - 1062

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