8R3X | pdb_00008r3x

Crystal structure of aPKC Iota kinase domain with LLGL2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.269 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.232 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8R3X

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: 86.94 kDa 
  • Atom Count: 5,721 
  • Modeled Residue Count: 700 
  • Deposited Residue Count: 752 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein kinase C iota type
A, B
356Homo 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
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LLGL scribble cell polarity complex component 2
C, D
20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P1M3 (Homo sapiens)
Explore Q6P1M3 
Go to UniProtKB:  Q6P1M3
PHAROS:  Q6P1M3
GTEx:  ENSG00000073350 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P1M3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.232 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.418α = 90
b = 86.324β = 90
c = 114.803γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: Database references
  • Version 1.2: 2025-04-23
    Changes: Database references