8SOI: Human ULK1 complex core

Structure of human ULK1 complex core (2:1:1 stoichiometry). Determined by electron microscopy at 4.2 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 4.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,243
Mol. weight: 167.54 kDa
Released: 21 Jun 2023

Explore 8SOI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SOI contains 48 α-helices and 22 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	12-16	5	1
α-helix	19-22	4
β-strand	24	1	2
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-46	4	1
α-helix	51	1
β-strand	52	1	1
α-helix	53-54	2
β-strand	58	1	2
α-helix	59-61	3
β-strand	66	1	3
β-strand	69	1	3
β-strand	71-75	5	1
α-helix	77-80	4
α-helix	84-86	3
α-helix	94-105	12
α-helix	112-179	68
α-helix	182-199	18
β-strand	203	1	4
α-helix	204-205	2
β-strand	307	1	4
α-helix	308-313	6
α-helix	321-334	14
α-helix	337-354	18
α-helix	357-360	4
α-helix	365-402	38
α-helix	408-542	135
α-helix	566-569	4
α-helix	579-588	10
α-helix	591-593	3

Chain B: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	12-16	5	5
α-helix	18-22	5
β-strand	24	1	6
α-helix	25-34	10
α-helix	40-42	3
β-strand	43-46	4	5
β-strand	52	1	5
β-strand	58	1	6
α-helix	70	1
β-strand	71-75	5	5
α-helix	76-80	5
α-helix	94-107	14
α-helix	112-199	88
β-strand	203	1	7
α-helix	208-211	4
α-helix	213-215	3
β-strand	307	1	7
α-helix	322-334	13
α-helix	337-354	18
α-helix	357-360	4
α-helix	365-403	39
α-helix	409-490	82
α-helix	492-542	51
β-strand	548	1	8
β-strand	552	1	8
α-helix	579-586	8

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	842-863	22
α-helix	880-890	11
α-helix	892-922	31
α-helix	931-970	40
α-helix	972-975	4
α-helix	976-996	21
α-helix	1003-1020	18
α-helix	1024-1043	20

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	463-470	8
α-helix	473-475	3
α-helix	488-513	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RB1-inducible coiled-coil protein 1	A, B	protein	600	Homo sapiens	Q8TDY2 (AlphaFold model)
Serine/threonine-protein kinase ULK1	C	protein	205	Homo sapiens	O75385 (AlphaFold model)
Autophagy-related protein 13	D	protein	61	Homo sapiens	O75143 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8SOI_1 RB1-inducible coiled-coil protein 1 (chains A, B)
MKLYVFLVNTGTTLTFDTELTVQTVADLKHAIQSKYKIAIQHQVLVVNGGECMAADRRVC
TYSAGTDTNPIFLFNKEMILCDRPPAIPKTTFSTENDMEIKVEESLMMPAVFHTVASRTQ
LALEMYEVAKKLCSFCEGLVHDEHLQHQGWAAIMANLEDCSNSYQKLLFKFESIYSNYLQ
SIEDIKLKLTHLGTAVSVMAKIPLLECLTRHSYRECLGRLDSLPEHEDSEKAEMKRSTEL
VLSPDMPRTTNESLLTSFPKSVEHVSPDTADAESGKEIRESCQSTVHQQDETTIDTKDGD
LPFFNVSLLDWINVQDRPNDVESLVRKCFDSMSRLDPRIIRPFIAECRQTIAKLDNQNMK
AIKGLEDRLYALDQMIASCGRLVNEQKELAQGFLANQKRAENLKDASVLPDLCLSHANQL
MIMLQNHRKLLDIKQKCTTAKQELANNLHVRLKWCCFVMLHADQDGEKLQALLRLVIELL
ERVKIVEALSTVPQMYCLAVVEVVRRKMFIKHYREWAGALVKDGKRLYEAEKSKRESFGK
LFRKSFLRNRLFRGLDSWPPSFCTQKPRKFDCELPDISLKDLQFLQSFCPSEVQPFLRVP

Sequence of entity 2 (C), FASTA

>8SOI_2 Serine/threonine-protein kinase ULK1 (chains C)
HTEILRGLRFTLLFVQHVLEIAALKGSASEAAGGPEYQLQESVVADQISLLSREWGFAEQ
LVLYLKVAELLSSGLQSAIDQIRAGKLCLSSTVKQVVRRLNELYKASVVSCQGLSLRLQR
FFLDKQRLLDRIHSITAERLIFSHAVQMVQSAALDEMFQHREGCVPRYHKALLLLEGLQH
MLSDQADIENVTKCKLCIERRLSAL

Sequence of entity 3 (D), FASTA

>8SOI_3 Autophagy-related protein 13 (chains D)
DLGTFYREFQNPPQLSSLSIDIGAQSMAEDLDSLPEKLAVHEKNVREFDAFVETLQGSDE
A

Primary citation

Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex. Chen, M., Ren, X., Cook, A. et al. bioRxiv (2023). DOI 10.1101/2023.06.01.543278

Other PDB entries of the same protein (UniProt Q8TDY2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7D0E 1.4 Å, Crystal structure of FIP200 Claw/p-CCPG1 FIR2
9D34 1.42 Å, FIP200 C-terminal CLAW domain (resid. 1490-1594) in complex with phosphorylated TNIP1…
8YFL 1.5 Å, crystal structure of FIP200 claw/TNIP1_FIR_pS122pS123
8YFM 1.5 Å, Crystal structure of FIP200 claw/TNIP1_FIR_pS122
6DCE 1.56 Å, X-ray structure of FIP200 claw domain
9J54 1.61 Å, Crystal structure of FIP200 Claw in complex with ATG16L1
7CZG 1.8 Å, Crystal structure of FIP200 Claw domain apo form
9LUA 1.97 Å, Crystal structure of FIP200 Claw domain and SMCR8 FIR motif complex
7CZM 2.0 Å, Crystal structure of FIP200 Claw/p-OPtineurin LIR complex
8YFK 2.0 Å, Crystal structure of FIP200 claw/TNIP1_FIR_pS123
7EA2 2.14 Å, crystal structure of NAP1 FIR in complex with RB1CC1 Claw domain
8YFN 2.3 Å, Crystal structure of FIP200 claw in complex with TNIP1_FIR_pS123 peptide with an…

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