8SQZ: RB1-inducible coiled-coil protein 1

Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture. Determined by electron microscopy at 5.85 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 5.85 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,438
Mol. weight: 229.23 kDa
Released: 21 Jun 2023

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

Secondary structure: helices and β-sheets

8SQZ contains 74 α-helices and 9 β-strands across 6 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: 24 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
β-strand	12	1	1
α-helix	18-22	5
α-helix	25-34	10
β-strand	47	1	2
β-strand	51	1	2
α-helix	59-62	4
α-helix	90-97	8
α-helix	119-173	55
α-helix	176-190	15
α-helix	192-201	10
α-helix	205-208	4
α-helix	308-315	8
α-helix	323-334	12
α-helix	347-353	7
α-helix	361-364	4
α-helix	366-383	18
α-helix	386-390	5
α-helix	393-403	11
α-helix	410-412	3
α-helix	414-462	49
α-helix	466-527	62
α-helix	528-533	6
α-helix	534-541	8
α-helix	550-552	3
α-helix	566-567	2
α-helix	570-572	3
α-helix	579-582	4

Chain B: 20 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	25-34	10
α-helix	37-39	3
β-strand	45-47	3	3
α-helix	63-64	2
β-strand	66	1	4
β-strand	69	1	4
β-strand	71-73	3	3
α-helix	90-91	2
α-helix	93-100	8
α-helix	101-105	5
α-helix	112-198	87
β-strand	206-209	4	5
α-helix	308-313	6
α-helix	322-324	3
α-helix	325-334	10
α-helix	337-353	17
α-helix	357-399	43
α-helix	408-543	136
α-helix	548-551	4
α-helix	566-567	2
α-helix	574-576	3
α-helix	578-585	8
α-helix	590-592	3
α-helix	593-596	4

Chain C: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	845-848	4
α-helix	850-859	10
α-helix	881-889	9
α-helix	892-916	25
α-helix	931-940	10
α-helix	943-955	13
α-helix	958-970	13
α-helix	972-973	2
α-helix	976-978	3
α-helix	979-993	15
α-helix	1004-1011	8
α-helix	1012-1015	4
α-helix	1017-1019	3
α-helix	1026-1043	18

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	843-864	22
α-helix	878-881	4
α-helix	883-889	7
α-helix	893-923	31
α-helix	932-962	31
α-helix	965-968	4
α-helix	976-996	21
α-helix	1004-1015	12
α-helix	1018-1021	4
α-helix	1031-1043	13

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	463-469	7
α-helix	473-475	3
α-helix	495-505	11
α-helix	507-511	5

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	463-469	7
α-helix	488-515	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RB1-inducible coiled-coil protein 1	A, B	protein	640	Homo sapiens	Q8TDY2 (AlphaFold model)
Serine/threonine-protein kinase ULK1	C, D	protein	215	Homo sapiens	O75385 (AlphaFold model)
Autophagy-related protein 13	E, F	protein	155	Homo sapiens	O75143 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8SQZ_1 RB1-inducible coiled-coil protein 1 (chains A, B)
MKLYVFLVNTGTTLTFDTELTVQTVADLKHAIQSKYKIAIQHQVLVVNGGECMAADRRVC
TYSAGTDTNPIFLFNKEMILCDRPPAIPKTTFSTENDMEIKVEESLMMPAVFHTVASRTQ
LALEMYEVAKKLCSFCEGLVHDEHLQHQGWAAIMANLEDCSNSYQKLLFKFESIYSNYLQ
SIEDIKLKLTHLGTAVSVMAKIPLLECLTRHSYRECLGRLDSLPEHEDSEKAEMKRSTEL
VLSPDMPRTTNESLLTSFPKSVEHVSPDTADAESGKEIRESCQSTVHQQDETTIDTKDGD
LPFFNVSLLDWINVQDRPNDVESLVRKCFDSMSRLDPRIIRPFIAECRQTIAKLDNQNMK
AIKGLEDRLYALDQMIASCGRLVNEQKELAQGFLANQKRAENLKDASVLPDLCLSHANQL
MIMLQNHRKLLDIKQKCTTAKQELANNLHVRLKWCCFVMLHADQDGEKLQALLRLVIELL
ERVKIVEALSTVPQMYCLAVVEVVRRKMFIKHYREWAGALVKDGKRLYEAEKSKRESFGK
LFRKSFLRNRLFRGLDSWPPSFCTQKPRKFDCELPDISLKDLQFLQSFCPSEVQPFLRVP
LLCDFEPLHQHVLALHNLVKAAQSLDEMSQTITDLLSEQK

Sequence of entity 2 (C, D), FASTA

>8SQZ_2 Serine/threonine-protein kinase ULK1 (chains C, D)
MEQEHTEILRGLRFTLLFVQHVLEIAALKGSASEAAGGPEYQLQESVVADQISLLSREWG
FAEQLVLYLKVAELLSSGLQSAIDQIRAGKLCLSSTVKQVVRRLNELYKASVVSCQGLSL
RLQRFFLDKQRLLDRIHSITAERLIFSHAVQMVQSAALDEMFQHREGCVPRYHKALLLLE
GLQHMLSDQADIENVTKCKLCIERRLSALLTGICA

Sequence of entity 3 (E, F), FASTA

>8SQZ_3 Autophagy-related protein 13 (chains E, F)
HDVLETIFVRKVGAFVNKPINQVTLTSLDIPFAMFAPKNLELEDTDPMVNPPDSPETESP
LQGSLHSDGSSGGSSGNTHDDFVMIDFKPAFSKDDILPMDLGTFYREFQNPPQLSSLSID
IGAQSMAEDLDSLPEKLAVHEKNVREFDAFVETLQ

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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