9C82 | pdb_00009c82

Structure of human ULK1C:PI3KC3-C1 supercomplex

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-06-11 Released: 2024-07-03 
  • Deposition Author(s): Chen, M., Hurley, J.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex.

Chen, M.Nguyen, T.N.Ren, X.Khuu, G.Cook, A.S.I.Zhao, Y.Yildiz, A.Lazarou, M.Hurley, J.H.

(2025) Nat Struct Mol Biol 32: 1596-1605

  • DOI: https://doi.org/10.1038/s41594-025-01557-x
  • Primary Citation of Related Structures:  
    9C82

  • PubMed Abstract: 

    The Unc-51-like kinase protein kinase complex (ULK1C) is the most upstream and central player in the initiation of macroautophagy in mammals. Here, we determined the cryo-electron microscopy structure of the human ULK1C core at amino-acid-level resolution. We also determined a moderate-resolution structure of the ULK1C core in complex with another autophagy core complex, the class III phosphatidylinositol 3-OH kinase complex I (PI3KC3-C1). We show that the two complexes coassemble through extensive contacts between the FIP200 scaffold subunit of ULK1C and the VPS15, ATG14 and BECN1 subunits of PI3KC3-C1. The FIP200:ATG13:ULK1 core of ULK1C undergoes a rearrangement from 2:1:1 to 2:2:2 stoichiometry in the presence of PI3KC3-C1. This suggests a structural mechanism for the initiation of autophagy through formation of a ULK1C:PI3KC3-C1 supercomplex and dimerization of ULK1 on the FIP200 scaffold.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoinositide 3-kinase regulatory subunit 41,358Homo sapiensMutation(s): 0 
Gene Names: PIK3R4VPS15
EC: 2.7.11.1
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Find proteins for Q99570 (Homo sapiens)
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PHAROS:  Q99570
GTEx:  ENSG00000196455 
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UniProt GroupQ99570
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3887Homo sapiensMutation(s): 0 
Gene Names: PIK3C3VPS34
EC: 2.7.1.137
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Find proteins for Q8NEB9 (Homo sapiens)
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PHAROS:  Q8NEB9
GTEx:  ENSG00000078142 
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UniProt GroupQ8NEB9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Beclin 1-associated autophagy-related key regulator492Homo sapiensMutation(s): 0 
Gene Names: ATG14
EC: 2.7.11.1
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Find proteins for O75385 (Homo sapiens)
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PHAROS:  O75385
GTEx:  ENSG00000177169 
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UniProt GroupO75385
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beclin-1450Homo sapiensMutation(s): 0 
Gene Names: BECN1GT197
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Find proteins for O75143 (Homo sapiens)
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PHAROS:  O75143
GTEx:  ENSG00000175224 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RB1-inducible coiled-coil protein 1E [auth F]640Homo sapiensMutation(s): 0 
Gene Names: RB1CC1KIAA0203RBICC
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Find proteins for Q8TDY2 (Homo sapiens)
Explore Q8TDY2 
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PHAROS:  Q8TDY2
GTEx:  ENSG00000023287 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111730
Michael J. Fox FoundationUnited StatesASAP-000350

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-10-01
    Changes: Data collection, Database references