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- PDB-5li9: Structure of a nucleotide-bound form of PKCiota core kinase domain -

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Basic information

Entry
Database: PDB / ID: 5li9
TitleStructure of a nucleotide-bound form of PKCiota core kinase domain
ComponentsProtein kinase C iota type
KeywordsTRANSFERASE / aPKC / Polarity / Complex
Function / homology
Function and homology information


Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / eye photoreceptor cell development / Schmidt-Lanterman incisure / cellular response to chemical stress ...Golgi vesicle budding / PAR polarity complex / Tight junction interactions / establishment of apical/basal cell polarity / protein kinase C / negative regulation of glial cell apoptotic process / diacylglycerol-dependent serine/threonine kinase activity / eye photoreceptor cell development / Schmidt-Lanterman incisure / cellular response to chemical stress / membrane organization / cell-cell junction organization / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of endothelial cell apoptotic process / tight junction / protein targeting to membrane / intercellular bridge / positive regulation of Notch signaling pathway / cell leading edge / regulation of postsynaptic membrane neurotransmitter receptor levels / brush border / bicellular tight junction / cytoskeleton organization / positive regulation of glial cell proliferation / vesicle-mediated transport / p75NTR recruits signalling complexes / response to interleukin-1 / secretion / actin filament organization / phospholipid binding / positive regulation of protein localization to plasma membrane / positive regulation of glucose import / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / Pre-NOTCH Transcription and Translation / cellular response to insulin stimulus / microtubule cytoskeleton / KEAP1-NFE2L2 pathway / cell migration / positive regulation of NF-kappaB transcription factor activity / negative regulation of neuron apoptotic process / endosome / protein kinase activity / intracellular signal transduction / apical plasma membrane / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding ...Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / 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. / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ACETATE ION / FORMIC ACID / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Protein kinase C iota type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsIvanova, M.E. / Purkiss, A.G. / McDonald, N.Q.
CitationJournal: Dev.Cell / Year: 2016
Title: aPKC Inhibition by Par3 CR3 Flanking Regions Controls Substrate Access and Underpins Apical-Junctional Polarization.
Authors: Soriano, E.V. / Ivanova, M.E. / Fletcher, G. / Riou, P. / Knowles, P.P. / Barnouin, K. / Purkiss, A. / Kostelecky, B. / Saiu, P. / Linch, M. / Elbediwy, A. / Kjr, S. / O'Reilly, N. / ...Authors: Soriano, E.V. / Ivanova, M.E. / Fletcher, G. / Riou, P. / Knowles, P.P. / Barnouin, K. / Purkiss, A. / Kostelecky, B. / Saiu, P. / Linch, M. / Elbediwy, A. / Kjr, S. / O'Reilly, N. / Snijders, A.P. / Parker, P.J. / Thompson, B.J. / McDonald, N.Q.
History
DepositionJul 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line ..._entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,93216
Polymers40,4811
Non-polymers1,45115
Water4,396244
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-10 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.806, 65.143, 87.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 40480.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCI, DXS1179E / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P41743, protein kinase C

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Non-polymers , 7 types, 259 molecules

#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 25% Morpheus precipitant mix 4, 10% Morpheus Carboxylic acids, Morpheus Buffer system 1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.79→52.233 Å / Num. obs: 33998 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.92 / Rmerge(I) obs: 0.163 / Net I/σ(I): 8.2
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.798 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A8W

3a8w


Resolution: 1.79→52.233 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1717 5.08 %Random Selection
Rwork0.1877 ---
obs0.19 33825 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.79→52.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 91 244 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042856
X-RAY DIFFRACTIONf_angle_d0.7653865
X-RAY DIFFRACTIONf_dihedral_angle_d12.3561698
X-RAY DIFFRACTIONf_chiral_restr0.048409
X-RAY DIFFRACTIONf_plane_restr0.004497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.84270.39441280.35762620X-RAY DIFFRACTION99
1.8427-1.90220.37151290.31852618X-RAY DIFFRACTION98
1.9022-1.97020.32621450.28222623X-RAY DIFFRACTION99
1.9702-2.0490.2511560.23242633X-RAY DIFFRACTION100
2.049-2.14230.261300.22542654X-RAY DIFFRACTION100
2.1423-2.25530.26241120.19752680X-RAY DIFFRACTION100
2.2553-2.39660.22171350.1882665X-RAY DIFFRACTION100
2.3966-2.58160.25111670.19812660X-RAY DIFFRACTION100
2.5816-2.84140.26751580.18772678X-RAY DIFFRACTION100
2.8414-3.25250.21961340.17092710X-RAY DIFFRACTION100
3.2525-4.09750.19731680.13842713X-RAY DIFFRACTION100
4.0975-52.25540.17221550.15372854X-RAY DIFFRACTION100
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)
10.9757-0.25970.48361.3006-0.60442.005-0.0220.03370.050.003-0.0798-0.11550.0430.1340.0770.0779-0.00580.00140.12420.00550.12253.67793.2698-7.0829
22.0187-0.12030.48162.3142-0.35181.83140.027-0.1445-0.06890.1329-0.03290.10190.0041-0.0560.0180.10830.0006-0.00340.1109-0.00790.0902-16.7438-0.8005-17.1966
31.9982-0.04830.04672.4185-0.5412.1449-0.04520.0873-0.0696-0.01850.04180.1433-0.004-0.1540.00740.12490.0273-0.04270.1517-0.04110.155-25.1880.4509-27.7582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 238 through 330)
2X-RAY DIFFRACTION2chain 'A' and (resid 343 through 467 )
3X-RAY DIFFRACTION3chain 'A' and (resid 468 through 513 )

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