9CE3 | pdb_00009ce3

Structure of the TSC:WIPI3 lysosomal recruitment complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9CE3

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: 737 kDa 
  • Atom Count: 35,086 
  • Modeled Residue Count: 4,379 
  • Deposited Residue Count: 6,607 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 4 of Tuberin
A, B
1,792Homo sapiensMutation(s): 0 
Gene Names: TSC2TSC4
UniProt & NIH Common Fund Data Resources
Find proteins for P49815 (Homo sapiens)
Explore P49815 
Go to UniProtKB:  P49815
PHAROS:  P49815
GTEx:  ENSG00000103197 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49815
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hamartin
C, D
1,191Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
TBC1 domain family member 7301Homo sapiensMutation(s): 0 
Gene Names: TBC1D7TBC7HSPC239
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0N9 (Homo sapiens)
Explore Q9P0N9 
Go to UniProtKB:  Q9P0N9
PHAROS:  Q9P0N9
GTEx:  ENSG00000145979 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P0N9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat domain phosphoinositide-interacting protein 3316Homo 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
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown fragment
G, H
12Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH-19-1-0182
Australian Research Council (ARC)AustraliaDE240100992
Australian Research Council (ARC)AustraliaLE170100016

Revision History  (Full details and data files)

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