8R3Y | pdb_00008r3y

Cryo EM structure of a stable LGL/aPKC Iota/Par-6 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8R3Y

This is version 1.2 of the entry. See complete history

Literature

Capture, mutual inhibition and release mechanism for aPKC-Par6 and its multisite polarity substrate Lgl.

Earl, C.P.Cobbaut, M.Barros-Carvalho, A.Ivanova, M.E.Briggs, D.C.Morais-de-Sa, E.Parker, P.J.McDonald, N.Q.

(2025) Nat Struct Mol Biol 32: 729-739

  • DOI: https://doi.org/10.1038/s41594-024-01425-0
  • Primary Citation Related Structures: 
    8R3X, 8R3Y

  • PubMed Abstract: 

    The mutually antagonistic relationship of atypical protein kinase C (aPKC) and partitioning-defective protein 6 (Par6) with the substrate lethal (2) giant larvae (Lgl) is essential for regulating polarity across many cell types. Although aPKC-Par6 phosphorylates Lgl at three serine sites to exclude it from the apical domain, aPKC-Par6 and Lgl paradoxically form a stable kinase-substrate complex, with conflicting roles proposed for Par6. We report the structure of human aPKCι-Par6α bound to full-length Llgl1, captured through an aPKCι docking site and a Par6 PDZ contact. This complex traps a phospho-S663 Llgl1 intermediate bridging between aPKC and Par6, impeding phosphorylation progression. Thus, aPKCι is effectively inhibited by Llgl1 pS663 while Llgl1 is captured by aPKCι-Par6. Mutational disruption of the Lgl-aPKC interaction impedes complex assembly and Lgl phosphorylation, whereas disrupting the Lgl-Par6 PDZ contact promotes complex dissociation and Lgl phosphorylation. We demonstrate a Par6 PDZ -regulated substrate capture-and-release model requiring binding by active Cdc42 and the apical partner Crumbs to drive complex disassembly. Our results suggest a mechanism for mutual regulation and spatial control of aPKC-Par6 and Lgl activities.


  • Organizational Affiliation
    • Signalling and Structural Biology Laboratory, Francis Crick Institute, London, UK.

Macromolecule Content 

  • Total Structure Weight: 152.4 kDa 
  • Atom Count: 10,132 
  • Modeled Residue Count: 1,293 
  • Deposited Residue Count: 1,374 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein kinase C iota typeA [auth I]338Homo sapiensMutation(s): 0 
Gene Names: PRKCIDXS1179E
EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for P41743 (Homo sapiens)
Explore P41743 
Go to UniProtKB:  P41743
PHAROS:  P41743
GTEx:  ENSG00000163558 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41743
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lethal(2) giant larvae protein homolog 1B [auth L]937Homo sapiensMutation(s): 0 
Gene Names: LLGL1DLG4HUGLHUGL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15334 (Homo sapiens)
Explore Q15334 
Go to UniProtKB:  Q15334
PHAROS:  Q15334
GTEx:  ENSG00000131899 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15334
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Partitioning defective 6 homolog alphaC [auth P]99Homo sapiensMutation(s): 0 
Gene Names: PARD6APAR6A
UniProt & NIH Common Fund Data Resources
Find proteins for R4GMM2 (Homo sapiens)
Explore R4GMM2 
Go to UniProtKB:  R4GMM2
GTEx:  ENSG00000102981 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4GMM2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP



Download:Ideal Coordinates CCD File
D [auth I]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A [auth I]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SEP
Query on SEP
B [auth L]L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomCC2068
Cancer Research UKUnited KingdomCC2026
Medical Research Council (MRC, United Kingdom)United KingdomCC2068

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-23
    Changes: Data collection, Database references