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- PDB-5li1: Structure of a Par3-inhibitory peptide bound to PKCiota core kina... -

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Basic information

Entry
Database: PDB / ID: 5li1
TitleStructure of a Par3-inhibitory peptide bound to PKCiota core kinase domain
Components
  • Par-3 partitioning defective 3 homolog (C. elegans)
  • Protein 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 / eye photoreceptor cell development / diacylglycerol-dependent serine/threonine kinase activity / 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 / eye photoreceptor cell development / diacylglycerol-dependent serine/threonine kinase activity / Schmidt-Lanterman incisure / cellular response to chemical stress / membrane organization / positive regulation of endothelial cell apoptotic process / cell-cell junction organization / tight junction / establishment or maintenance of epithelial cell apical/basal polarity / 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 / vesicle-mediated transport / positive regulation of glial cell proliferation / cytoskeleton organization / p75NTR recruits signalling complexes / response to interleukin-1 / secretion / positive regulation of glucose import / positive regulation of protein localization to plasma membrane / actin filament organization / Schaffer collateral - CA1 synapse / phospholipid binding / Pre-NOTCH Transcription and Translation / positive regulation of neuron projection development / 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 / protein kinase activity / intracellular signal transduction / endosome / 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 / nucleus / metal ion binding / 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. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Protein kinase C iota type / Par-3 partitioning defective 3 homolog (C. elegans)
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSoriano, E.V. / 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 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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
B: Par-3 partitioning defective 3 homolog (C. elegans)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9917
Polymers43,3052
Non-polymers6865
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-35 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.030, 82.030, 90.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 40914.934 Da / Num. of mol.: 1 / Fragment: UNP residues 246-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKCI, DXS1179E / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41743, protein kinase C
#2: Protein/peptide Par-3 partitioning defective 3 homolog (C. elegans) / Uncharacterized protein


Mass: 2389.712 Da / Num. of mol.: 1 / Fragment: UNP residues 816-835
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: pard3, TEgg053l09.1-001 / Production host: synthetic construct (others) / References: UniProt: Q28E03

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Non-polymers , 5 types, 202 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% Peg 2000 MME, 0.08 M KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→41.01 Å / Num. obs: 25607 / % possible obs: 99.5 % / Redundancy: 5.6 % / Rpim(I) all: 0.031 / Net I/σ(I): 8.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.4 / Rpim(I) all: 0.233 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A8W

3a8w


Resolution: 2→41.01 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.15
RfactorNum. reflection% reflection
Rfree0.2168 1238 5.11 %
Rwork0.1504 --
obs0.1537 24233 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 36 197 3073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082985
X-RAY DIFFRACTIONf_angle_d1.0954049
X-RAY DIFFRACTIONf_dihedral_angle_d13.7131116
X-RAY DIFFRACTIONf_chiral_restr0.084430
X-RAY DIFFRACTIONf_plane_restr0.004523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.27381220.17952516X-RAY DIFFRACTION99
2.0801-2.17480.25721330.16872499X-RAY DIFFRACTION99
2.1748-2.28940.25231370.15822520X-RAY DIFFRACTION100
2.2894-2.43290.21591580.15992500X-RAY DIFFRACTION100
2.4329-2.62070.27731480.16062537X-RAY DIFFRACTION100
2.6207-2.88430.24531410.1622545X-RAY DIFFRACTION100
2.8843-3.30160.22261150.15332599X-RAY DIFFRACTION100
3.3016-4.1590.17881560.13012564X-RAY DIFFRACTION100
4.159-41.02360.19321280.14542715X-RAY DIFFRACTION99
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)
12.84411.0151-0.6533.39640.30071.74120.04730.11730.1923-0.07460.0128-0.1663-0.1366-0.0093-0.05110.1221-0.02360.0040.1417-0.01550.131-21.36076.416714.7719
21.207-0.0390.121.7733-0.15031.9613-0.0222-0.0152-0.0643-0.04290.0127-0.03190.0786-0.0530.00440.1126-0.01620.00060.13230.0030.111-32.3222-15.139510.1864
31.82451.1927-1.72968.2491-3.24582.7193-0.15460.0395-0.1798-0.1974-0.1109-0.84340.11240.19890.33870.1163-0.01140.00640.3133-0.03730.3115-8.8576-1.459310.3423
44.94333.6003-3.84787.6385-5.81874.85360.09850.22010.57430.38290.07250.3937-0.8068-0.2602-0.20610.23550.00990.0070.1702-0.02350.2456-24.225417.016912.3436
52.13530.96770.12941.4061-0.3423.1230.10380.320.4638-0.3028-0.0664-0.639-0.18430.2099-0.01620.2151-0.04760.03160.22490.00750.2456-24.3332-5.0583-1.1893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 249 through 332 )
2X-RAY DIFFRACTION2chain 'A' and (resid 333 through 541 )
3X-RAY DIFFRACTION3chain 'A' and (resid 542 through 567 )
4X-RAY DIFFRACTION4chain 'A' and (resid 568 through 589 )
5X-RAY DIFFRACTION5chain 'B'

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