8SLZ

Crystal structure of phosphorylated (T357/S358) human MLKL pseudokinase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Phosphorylation-dependent pseudokinase domain dimerization drives full-length MLKL oligomerization.

Meng, Y.Garnish, S.E.Davies, K.A.Black, K.A.Leis, A.P.Horne, C.R.Hildebrand, J.M.Hoblos, H.Fitzgibbon, C.Young, S.N.Dite, T.Dagley, L.F.Venkat, A.Kannan, N.Koide, A.Koide, S.Glukhova, A.Czabotar, P.E.Murphy, J.M.

(2023) Nat Commun 14: 6804-6804

  • DOI: https://doi.org/10.1038/s41467-023-42255-w
  • Primary Citation of Related Structures:  
    8SLZ

  • PubMed Abstract: 

    The necroptosis pathway is a lytic, pro-inflammatory mode of cell death that is widely implicated in human disease, including renal, pulmonary, gut and skin inflammatory pathologies. The precise mechanism of the terminal steps in the pathway, where the RIPK3 kinase phosphorylates and triggers a conformation change and oligomerization of the terminal pathway effector, MLKL, are only emerging. Here, we structurally identify RIPK3-mediated phosphorylation of the human MLKL activation loop as a cue for MLKL pseudokinase domain dimerization. MLKL pseudokinase domain dimerization subsequently drives formation of elongated homotetramers. Negative stain electron microscopy and modelling support nucleation of the MLKL tetramer assembly by a central coiled coil formed by the extended, ~80 Å brace helix that connects the pseudokinase and executioner four-helix bundle domains. Mutational data assert MLKL tetramerization as an essential prerequisite step to enable the release and reorganization of four-helix bundle domains for membrane permeabilization and cell death.


  • Organizational Affiliation

    Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mixed lineage kinase domain-like protein287Homo sapiensMutation(s): 0 
Gene Names: MLKL
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB16 (Homo sapiens)
Explore Q8NB16 
Go to UniProtKB:  Q8NB16
PHAROS:  Q8NB16
GTEx:  ENSG00000168404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NB16
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.811α = 90
b = 74.961β = 90
c = 127.227γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1172929

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary