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

Validation slider image for 9C82

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 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.

Macromolecule Content 

  • Total Structure Weight: 435.64 kDa 
  • Atom Count: 11,172 
  • Modeled Residue Count: 2,254 
  • Deposited Residue Count: 3,827 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphoinositide 3-kinase regulatory subunit 41,358Homo sapiensMutation(s): 0 
Gene Names: PIK3R4VPS15
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99570 (Homo sapiens)
Explore Q99570 
Go to UniProtKB:  Q99570
PHAROS:  Q99570
GTEx:  ENSG00000196455 
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UniProt GroupQ99570
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase catalytic subunit type 3887Homo sapiensMutation(s): 0 
Gene Names: PIK3C3VPS34
EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEB9 (Homo sapiens)
Explore Q8NEB9 
Go to UniProtKB:  Q8NEB9
PHAROS:  Q8NEB9
GTEx:  ENSG00000078142 
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UniProt GroupQ8NEB9
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Reference Sequence
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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
UniProt & NIH Common Fund Data Resources
Find proteins for O75385 (Homo sapiens)
Explore O75385 
Go to UniProtKB:  O75385
PHAROS:  O75385
GTEx:  ENSG00000177169 
Entity Groups
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UniProt GroupO75385
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Beclin-1450Homo sapiensMutation(s): 0 
Gene Names: BECN1GT197
UniProt & NIH Common Fund Data Resources
Find proteins for O75143 (Homo sapiens)
Explore O75143 
Go to UniProtKB:  O75143
PHAROS:  O75143
GTEx:  ENSG00000175224 
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UniProt GroupO75143
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
RB1-inducible coiled-coil protein 1E [auth F]640Homo sapiensMutation(s): 0 
Gene Names: RB1CC1KIAA0203RBICC
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDY2 (Homo sapiens)
Explore Q8TDY2 
Go to UniProtKB:  Q8TDY2
PHAROS:  Q8TDY2
GTEx:  ENSG00000023287 
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UniProt GroupQ8TDY2
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Reference Sequence

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

View Full Validation Report



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