9C9I | pdb_00009c9i

Structure of the TSC1:WIPI3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 
    0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Structure of the human TSC:WIPI3 lysosomal recruitment complex.

Bayly-Jones, C.Lupton, C.J.D'Andrea, L.Chang, Y.G.Jones, G.D.Steele, J.R.Venugopal, H.Schittenhelm, R.B.Halls, M.L.Ellisdon, A.M.

(2024) Sci Adv 10: eadr5807-eadr5807

  • DOI: https://doi.org/10.1126/sciadv.adr5807
  • Primary Citation Related Structures: 
    9C9I, 9CE3

  • PubMed Abstract: 

    Tuberous sclerosis complex (TSC) is targeted to the lysosomal membrane, where it hydrolyzes RAS homolog-mTORC1 binding (RHEB) from its GTP-bound to GDP-bound state, inhibiting mechanistic target of rapamycin complex 1 (mTORC1). Loss-of-function mutations in TSC cause TSC disease, marked by excessive tumor growth. Here, we overcome a high degree of continuous conformational heterogeneity to determine the 2.8-Å cryo-electron microscopy (cryo-EM) structure of the complete human TSC in complex with the lysosomal recruitment factor WD repeat domain phosphoinositide-interacting protein 3 (WIPI3). We discover a previously undetected amino-terminal TSC1 HEAT repeat dimer that clamps onto a single TSC wing and forms a phosphatidylinositol phosphate (PIP)-binding pocket, which specifically binds monophosphorylated PIPs. These structural advances provide a model by which WIPI3 and PIP-signaling networks coordinate to recruit TSC to the lysosomal membrane to inhibit mTORC1. The high-resolution TSC structure reveals previously unrecognized mutational hotspots and uncovers crucial insights into the mechanisms of TSC dysregulation in disease.


  • Organizational Affiliation
    • Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.

Macromolecule Content 

  • Total Structure Weight: 158.34 kDa 
  • Atom Count: 10,118 
  • Modeled Residue Count: 1,304 
  • Deposited Residue Count: 1,434 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat domain phosphoinositide-interacting protein 3A,
B [auth C],
C [auth E],
D [auth G]
316Homo sapiensMutation(s): 0 
Gene Names: WDR45BWDR45LWIPI3
UniProt & NIH Common Fund Data Resources
Find proteins for Q5MNZ6 (Homo sapiens)
Explore Q5MNZ6 
Go to UniProtKB:  Q5MNZ6
PHAROS:  Q5MNZ6
GTEx:  ENSG00000141580 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5MNZ6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HamartinE [auth X],
F [auth B],
G [auth D],
H [auth F],
I [auth H]
34Homo sapiensMutation(s): 0 
Gene Names: TSC1KIAA0243TSC
UniProt & NIH Common Fund Data Resources
Find proteins for Q92574 (Homo sapiens)
Explore Q92574 
Go to UniProtKB:  Q92574
PHAROS:  Q92574
GTEx:  ENSG00000165699 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92574
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.241α = 90
b = 94.241β = 90
c = 199.386γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesTS180061

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release