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- EMDB-48106: Lgl2 bound to the aPKCiota-Par6a complex in its nucleotide-free form. -

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Basic information

Entry
Database: EMDB / ID: EMD-48106
TitleLgl2 bound to the aPKCiota-Par6a complex in its nucleotide-free form.
Map data
Sample
  • Complex: A ternary complex of Lgl2 with aPKC iota and Par6A (nucleotide-free)
    • Protein or peptide: Lethal Giant Larvae homolog 2 (Lgl2)
    • Protein or peptide: Atypical protein kinase C (aPKC) iota
    • Protein or peptide: Partitioning defective 6 homolog alpha (Par6A)
KeywordsCell Polarity / Kinase / Complex. / LIPID BINDING PROTEIN
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
Protein kinase C iota type / LLGL scribble cell polarity complex component 2 / Isoform 2 of Partitioning defective 6 homolog alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsAlmagor L / Weis WI
Funding support1 items
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 WI
History
DepositionNov 28, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48106.png

Downloads & links

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Map

FileDownload / File: emd_48106.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.56 Å/pix.
x 512 pix.
= 284.416 Å		0.56 Å/pix.
x 512 pix.
= 284.416 Å		0.56 Å/pix.
x 512 pix.
= 284.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5555 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.1537727 - 0.24698307
Average (Standard dev.)-0.000067120265 (±0.0059106736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 284.416 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48106_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48106_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A ternary complex of Lgl2 with aPKC iota and Par6A (nucleotide-free)

EntireName: A ternary complex of Lgl2 with aPKC iota and Par6A (nucleotide-free)
Components
  • Complex: A ternary complex of Lgl2 with aPKC iota and Par6A (nucleotide-free)
    • Protein or peptide: Lethal Giant Larvae homolog 2 (Lgl2)
    • Protein or peptide: Atypical protein kinase C (aPKC) iota
    • Protein or peptide: Partitioning defective 6 homolog alpha (Par6A)

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Supramolecule #1: A ternary complex of Lgl2 with aPKC iota and Par6A (nucleotide-free)

SupramoleculeName: A ternary complex of Lgl2 with aPKC iota and Par6A (nucleotide-free)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 216.9931 KDa

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Macromolecule #1: Lethal Giant Larvae homolog 2 (Lgl2)

MacromoleculeName: Lethal Giant Larvae homolog 2 (Lgl2) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRERLKRDLF QFNKTVEHGF PHQPSALGYS PSLRILAIGT RSGAIKLYGA PGVEFMGLHQ ENNAVTQIHL LPGQCQLVTL LDDNSLHLWS L KVKGGASE LQEDESFTLR GPPGAAPSAT QITVVLPHSS CELLYLGTES GNVFVVQLPA FRALEDRTIS SDAVLQRLPE ...String:
MRERLKRDLF QFNKTVEHGF PHQPSALGYS PSLRILAIGT RSGAIKLYGA PGVEFMGLHQ ENNAVTQIHL LPGQCQLVTL LDDNSLHLWS L KVKGGASE LQEDESFTLR GPPGAAPSAT QITVVLPHSS CELLYLGTES GNVFVVQLPA FRALEDRTIS SDAVLQRLPE EARHRRVFEM VE ALQEHPR DPNQILIGYS RGLVVIWDLQ GSRVLYHFLS SQQLENIWWQ RDGRLLVSCH SDGSYCQWPV SSEAQQPEPL RSLVPYGPFP CKA ITRILW LTTRQGLPFT IFQGGMPRAS YGDRHCISVI HDGQQTAFDF TSRVIGFTVL TEADPAATFD DPYALVVLAE EELVVIDLQT AGWP PVQLP YLASLHCSAI TCSHHVSNIP LKLWERIIAA GSRQNAHFST MEWPIDGGTS LTPAPPQRDL LLTGHEDGTV RFWDASGVCL RLLYK LSTV RVFLTDTDPN ENFSAQGEDE WPPLRKVGSF DPYSDDPRLG IQKIFLCKYS GYLAVAGTAG QVLVLELNDE AAEQAVEQVE ADLLQD QEG YRWKGHERLA ARSGPVRFEP GFQPFVLVQC QPPAVVTSLA LHSEWRLVAF GTSHGFGLFD HQQRRQVFVK CTLHPSDQLA LEGPLSR VK SLKKSLRQSF RRMRRSRVSS RKRHPAGPPG EAQEGSAKAE RPGLQNMELA PVQRKIEARS AEDSFTGFVR TLYFADTYLK DSSRHCPS L WAGTNGGTIY AFSLRVPPAE RRMDEPVRAE QAKEIQLMHR APVVGILVLD GHSVPLPEPL EVAHDLSKSP DMQGSHQLLV VSEEQFKVF TLPKVSAKLK LKLTALEGSR VRRVSVAHFG SRRAEDYGEH HLAVLTNLGD IQVVSLPLLK PQVRYSCIRR EDVSGIASCV FTKYGQGFYL ISPSEFERF SLSTKWLVEP RCLVDSAETK NHRPGNGAGP KKAPSRARNS GTQSDGEEKQ PGLVMEREFT TASHHHHHHG ENLYFQ

UniProtKB: LLGL scribble cell polarity complex component 2

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Macromolecule #2: Atypical protein kinase C (aPKC) iota

MacromoleculeName: Atypical protein kinase C (aPKC) iota / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: protein kinase C
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPTQRDSSTM SHTVAGGGSG DHSHQVRVKA YYRGDIMITH FEPSISFEGL CNEVRDMCSF DNEQLFTMKW IDEEGDPCTV SSQLELEEAF RLYELNKDSE LLIHVFPCVP ERPGMPCPGE DKSIYRRGAR RWRKLYCANG HTFQAKRFNR RAHCAICTDR IWGLGRQGYK ...String:
MPTQRDSSTM SHTVAGGGSG DHSHQVRVKA YYRGDIMITH FEPSISFEGL CNEVRDMCSF DNEQLFTMKW IDEEGDPCTV SSQLELEEAF RLYELNKDSE LLIHVFPCVP ERPGMPCPGE DKSIYRRGAR RWRKLYCANG HTFQAKRFNR RAHCAICTDR IWGLGRQGYK CINCKLLVHK KCHKLVTIEC GRHSLPQEPV MPMDQSSMHS DHAQTVIPYN PSSHESLDQV GEEKEAMNTR ESGKASSSLG LQDFDLLRVI GRGSYAKVLL VRLKKTDRIY AMKVVKKELV NDDEDIDWVQ TEKHVFEQAS NHPFLVGLHS CFQTESRLFF VIEYVNGGDL MFHMQRQRKL PEEHARFYSA EISLALNYLH ERGIIYRDLK LDNVLLDSEG HIKLTDYGMC KEGLRPGDTT S(TPO)FCGTPNYI APEILRGEDY GFSVDWWALG VLMFEMMAGR SPFDIVGSSD NPDQNTEDYL FQVILEKQIR IPRSLSVKAA SVLKSFLNKD PKERLGCHPQ TGFADIQGHP FFRNVDWDMM EQKQVVPPFK PNISGEFGLD NFDSQFTNEP VQL(TPO)PDDDDI VRKIDQSEFE GFEYINPLLM SAEECV

UniProtKB: Protein kinase C iota type

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Macromolecule #3: Partitioning defective 6 homolog alpha (Par6A)

MacromoleculeName: Partitioning defective 6 homolog alpha (Par6A) / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MARPQRTPAR SPDSIVEVKS KFDAEFRRFA LPRASVSGFQ EFSRLLRAVH QIPGLDVLLG YTDAHGDLLP LTNDDSLHRA LASGPPPLRL LVQKREADSS GLAFASNSLQ RRKKGLLLRP VAPLRTRPPL LISLPQDFRQ VSSVIDVDLL PETHRRVRLH KHGSDRPLGF ...String:
MARPQRTPAR SPDSIVEVKS KFDAEFRRFA LPRASVSGFQ EFSRLLRAVH QIPGLDVLLG YTDAHGDLLP LTNDDSLHRA LASGPPPLRL LVQKREADSS GLAFASNSLQ RRKKGLLLRP VAPLRTRPPL LISLPQDFRQ VSSVIDVDLL PETHRRVRLH KHGSDRPLGF YIRDGMSVRV APQGLERVPG IFISRLVRGG LAESTGLLAV SDEILEVNGI EVAGKTLDQV TDMMVANSHN LIVTVKPANQ RNNVVRGASG RLTGPPSAGP GPAEPDSDDD SSDLVIENRQ PPSSNGLSQG PPCWDLHPGC RHPGTRSSLP SLDDQEQASS GWGSRIRGDG SGFSLEFTTA SENLYFQ

UniProtKB: Isoform 2 of Partitioning defective 6 homolog alpha

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
Details: 20 mM Tris 200 mM NaCl 1 mM DTT 0.05% n-octyl-beta-D-glucoside
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
DetailsData collected at 40 degrees tilt
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.9 µm / Calibrated defocus min: 1.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction by cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 95801
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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