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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 / establishment or maintenance of polarity of embryonic epithelium / Golgi vesicle budding / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / PAR polarity complex / Tight junction interactions / regulation of establishment or maintenance of cell polarity / protein kinase C / establishment of apical/basal cell polarity / diacylglycerol-dependent serine/threonine kinase activity ...establishment of spindle orientation / establishment or maintenance of polarity of embryonic epithelium / Golgi vesicle budding / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / PAR polarity complex / Tight junction interactions / regulation of establishment or maintenance of cell polarity / protein kinase C / establishment of apical/basal cell polarity / diacylglycerol-dependent serine/threonine kinase activity / L-leucine transport / myosin II binding / negative regulation of glial cell apoptotic process / regulation of Notch signaling pathway / eye photoreceptor cell development / branching involved in labyrinthine layer morphogenesis / 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 / cortical actin cytoskeleton organization / protein targeting to membrane / labyrinthine layer blood vessel development / cortical actin cytoskeleton / positive regulation of Notch signaling pathway / establishment of cell polarity / cell leading edge / exocytosis / brush border / positive regulation of glial cell proliferation / positive regulation of endothelial cell apoptotic process / bicellular tight junction / regulation of postsynaptic membrane neurotransmitter receptor levels / p75NTR recruits signalling complexes / intercellular bridge / vesicle-mediated transport / cytoskeleton organization / secretion / response to interleukin-1 / GTPase activator activity / actin filament organization / post-embryonic development / protein localization to plasma membrane / positive regulation of D-glucose import / adherens junction / positive regulation of protein localization to plasma membrane / PDZ domain binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of neuron projection development / phospholipid binding / Pre-NOTCH Transcription and Translation / Schaffer collateral - CA1 synapse / multicellular organism growth / cellular response to insulin stimulus / KEAP1-NFE2L2 pathway / cell migration / microtubule cytoskeleton / negative regulation of neuron apoptotic process / protein phosphorylation / protein kinase activity / endosome / intracellular signal transduction / cilium / apical plasma membrane / Golgi membrane / cell division / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / 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. / WD domain, G-beta repeat / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeats / 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: Lior Almagor / William I Weis /
Abstract: Polarity along an apical-basal axis is essential for epithelial cell shape and function. The atypical protein Kinase-C (aPKC) and its regulatory partner Par6 form a complex that is essential for ...Polarity along an apical-basal axis is essential for epithelial cell shape and function. The atypical protein Kinase-C (aPKC) and its regulatory partner Par6 form a complex that is essential for polarization, a primary function of which is to phosphorylate the Lethal giant larvae (Lgl) protein to prevent it from binding to the apical membrane (thereby facilitating its basolateral localization). Par6 binds Lgl directly and is essential for this process, but its mechanism was obscure. Here, we utilize cryo-EM and various biochemical techniques to characterize the interaction of Lgl2 with the aPKCι/Par6 complex and to study the roles of Par6 in promoting Lgl2 phosphorylation. We find that Par6 proteins stabilize a ternary Lgl2/aPKCι/Par6 complex that involves a unique multi-surface interaction of Lgl2 with both aPKCι and Par6. Importantly, we find Par6b induces processive phosphorylation that results in a multi-phosphorylated Lgl2 after a single interaction with the aPKCι/Par6b complex. This is enabled by a Par6b/Lgl2 interaction that maintains contact of Lgl2 with the kinase throughout its distinct nucleotide-binding states. Our results reveal the mechanistic basis for the efficient regulation of Lgl's membrane binding by aPKC/Par6 and provide invaluable structural data for further understanding the mechanisms of this polarity complex.
History
DepositionNov 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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