9C82 | pdb_00009c82

Structure of human ULK1C:PI3KC3-C1 supercomplex

• PDB DOI: https://doi.org/10.2210/pdb9C82/pdb
• Entry: 9C82 supersedes: 8SRQ
• EM Map EMD-45297: EMDB EMDataResource

• 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

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Experimental Data Snapshot

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

Literature

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

Chen, M., Ren, X., Cook, A., Hurley, J.H.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.06.01.543278

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, assay for oligomerization

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoinositide 3-kinase regulatory subunit 4	A	1,358	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R4, VPS15 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase catalytic subunit type 3	B	887	Homo sapiens	Mutation(s): 0  Gene Names: PIK3C3, VPS34 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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin 1-associated autophagy-related key regulator	C	492	Homo sapiens	Mutation(s): 0  Gene Names: ATG14
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZNE5 (Homo sapiens) Explore Q6ZNE5  Go to UniProtKB:  Q6ZNE5
PHAROS:  Q6ZNE5 GTEx:  ENSG00000126775

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-1	D	450	Homo sapiens	Mutation(s): 0  Gene Names: BECN1, GT197
UniProt & NIH Common Fund Data Resources
Find proteins for Q14457 (Homo sapiens) Explore Q14457  Go to UniProtKB:  Q14457
PHAROS:  Q14457 GTEx:  ENSG00000126581

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RB1-inducible coiled-coil protein 1	E [auth F]	640	Homo sapiens	Mutation(s): 0  Gene Names: RB1CC1, KIAA0203, RBICC
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDY2 (Homo sapiens) Explore Q8TDY2  Go to UniProtKB:  Q8TDY2
PHAROS:  Q8TDY2 GTEx:  ENSG00000023287

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Chen, M., Hurley, J.H.
• This entry supersedes: 8SRQ

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111730
Michael J. Fox Foundation	United States	ASAP-000350

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release