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- PDB-9ejm: Lgl2 bound to the aPKCiota-Par6B complex in its ADP-bound form -

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Basic information

Entry
Database: PDB / ID: 9ejm
TitleLgl2 bound to the aPKCiota-Par6B complex in its ADP-bound form
Components
  • LLGL scribble cell polarity complex component 2
  • Partitioning defective 6 homolog beta
  • Protein kinase C iota type
KeywordsLIPID BINDING PROTEIN / Cell Polarity / Kinase / Complex
Function / homology
Function and homology information


establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / Golgi vesicle budding / PAR polarity complex / Tight junction interactions / calcium,diacylglycerol-dependent serine/threonine kinase activity / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / establishment of apical/basal cell polarity ...establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / Golgi vesicle budding / PAR polarity complex / Tight junction interactions / calcium,diacylglycerol-dependent serine/threonine kinase activity / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / establishment of apical/basal cell polarity / L-leucine transport / negative regulation of glial cell apoptotic process / regulation of Notch signaling pathway / eye photoreceptor cell development / myosin II binding / Schmidt-Lanterman incisure / Golgi to plasma membrane transport / establishment or maintenance of epithelial cell apical/basal polarity / cellular response to chemical stress / membrane organization / cell-cell junction organization / tight junction / protein targeting to membrane / cortical actin cytoskeleton organization / cortical actin cytoskeleton / positive regulation of Notch signaling pathway / establishment of cell polarity / cell leading edge / exocytosis / brush border / positive regulation of endothelial cell apoptotic process / bicellular tight junction / regulation of postsynaptic membrane neurotransmitter receptor levels / intercellular bridge / vesicle-mediated transport / positive regulation of glial cell proliferation / cytoskeleton organization / response to interleukin-1 / p75NTR recruits signalling complexes / secretion / GTPase activator activity / actin filament organization / protein localization to plasma membrane / positive regulation of D-glucose import / PDZ domain binding / adherens junction / positive regulation of protein localization to plasma membrane / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / phospholipid binding / Pre-NOTCH Transcription and Translation / cellular response to insulin stimulus / positive regulation of NF-kappaB transcription factor activity / KEAP1-NFE2L2 pathway / cell migration / microtubule cytoskeleton / 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 / negative regulation of apoptotic process / glutamatergic synapse / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Lethal(2) giant larvae protein / Lethal giant larvae homologue 2 / LLGL2 / Atypical protein kinase C iota type, catalytic domain / Protein kinase C / Protein kinase C, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : ...Lethal(2) giant larvae protein / Lethal giant larvae homologue 2 / LLGL2 / 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. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeat / WD40-repeat-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein kinase C iota type / LLGL scribble cell polarity complex component 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsAlmagor, L. / Weis, W.I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2025
Title: Polarity protein Par6 facilitates the processive phosphorylation of Lgl via a dynamic interaction with aPKC
Authors: Almagor, L. / Weis, W.I.
History
DepositionNov 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LLGL scribble cell polarity complex component 2
B: Protein kinase C iota type
C: Partitioning defective 6 homolog beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,7985
Polymers220,3473
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein LLGL scribble cell polarity complex component 2 / HGL / Lethal(2) giant larvae protein homolog 2


Mass: 109362.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LLGL2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6P1M3
#2: Protein Protein kinase C iota type / Atypical protein kinase C-lambda/iota / PRKC-lambda/iota / aPKC-lambda/iota / nPKC-iota


Mass: 68512.258 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): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41743, protein kinase C
#3: Protein Partitioning defective 6 homolog beta


Mass: 42472.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pard6b, Par6b / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1A ternary complex of Lgl2 with aPKC iota and Par6B (ADP-bound)COMPLEX#1-#30RECOMBINANT
2A ternary complex of Lgl2 with aPKC iota and Par6B (ADP-bound)COMPLEX#31RECOMBINANT
3A ternary complex of Lgl2 with aPKC iota and Par6B (ADP-bound)COMPLEX#1-#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Mus musculus (house mouse)10090
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 20 mM Tris 200 mM NaCl 1 mM DTT 10 mM MgCl2 1 mM ADP 10 uM ZnCl2 0.05% n-octyl-beta-D-glucoside
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Data collected at both 25 and 40 degrees tilt
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1300 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 787439 / Symmetry type: POINT

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