8SOI | pdb_00008soi

Structure of human ULK1 complex core (2:1:1 stoichiometry)

• PDB DOI: https://doi.org/10.2210/pdb8SOI/pdb
• EM Map EMD-40658: EMDB EMDataResource

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


• Deposited: 2023-04-28 Released: 2023-06-21 
• 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: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

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 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 167.54 kDa 
• Atom Count: 10,243 
• Modeled Residue Count: 1,276 
• Deposited Residue Count: 1,466 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RB1-inducible coiled-coil protein 1	A, B	600	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase ULK1	C	205	Homo sapiens	Mutation(s): 0  Gene Names: ULK1, KIAA0722 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 13	D	61	Homo sapiens	Mutation(s): 0  Gene Names: ATG13, KIAA0652
UniProt & NIH Common Fund Data Resources
Find proteins for O75143 (Homo sapiens) Explore O75143  Go to UniProtKB:  O75143
PHAROS:  O75143 GTEx:  ENSG00000175224

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.1
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Chen, M., Hurley, J.H.

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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: 2023-06-21
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary