8SRM: RB1-inducible coiled-coil protein 1
Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant. Determined by electron microscopy at 4.46 Å resolution. Released 21 Jun 2023.
- Method
- Electron microscopy
- Resolution
- 4.46 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 5,773
- Mol. weight
- 211.33 kDa
- Released
- 21 Jun 2023
Explore 8SRM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8SRM contains 57 α-helices and 11 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: 21 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 1 |
| α-helix | 8-10 | 3 | |
| β-strand | 14-16 | 3 | 1 |
| α-helix | 18-22 | 5 | |
| β-strand | 24 | 1 | 2 |
| α-helix | 25-32 | 8 | |
| α-helix | 40-42 | 3 | |
| β-strand | 44-46 | 3 | 3 |
| β-strand | 52 | 1 | 3 |
| β-strand | 58 | 1 | 2 |
| α-helix | 59-62 | 4 | |
| α-helix | 70-71 | 2 | |
| β-strand | 72-74 | 3 | 3 |
| α-helix | 76-79 | 4 | |
| α-helix | 128-201 | 74 | |
| β-strand | 203 | 1 | 4 |
| α-helix | 206-211 | 6 | |
| β-strand | 307 | 1 | 4 |
| α-helix | 308-314 | 7 | |
| α-helix | 317-319 | 3 | |
| α-helix | 321-334 | 14 | |
| α-helix | 337-363 | 27 | |
| α-helix | 368-386 | 19 | |
| α-helix | 425-488 | 64 | |
| α-helix | 489-491 | 3 | |
| α-helix | 492-542 | 51 | |
| α-helix | 548-551 | 4 | |
| α-helix | 575-576 | 2 | |
| α-helix | 579-588 | 10 | |
| α-helix | 591-596 | 6 | |
Chain B: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 161-201 | 41 | |
| β-strand | 203 | 1 | 5 |
| β-strand | 307 | 1 | 5 |
| α-helix | 308-315 | 8 | |
| α-helix | 321-334 | 14 | |
| α-helix | 340-350 | 11 | |
| α-helix | 463-540 | 78 | |
| α-helix | 557-560 | 4 | |
| α-helix | 562-564 | 3 | |
| α-helix | 566-567 | 2 | |
| α-helix | 579-588 | 10 | |
Chain C: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 841-865 | 25 | |
| α-helix | 870-872 | 3 | |
| α-helix | 878-890 | 13 | |
| α-helix | 892-922 | 31 | |
| α-helix | 930-963 | 34 | |
| α-helix | 965-970 | 6 | |
| α-helix | 972-973 | 2 | |
| α-helix | 976-995 | 20 | |
| α-helix | 1003-1019 | 17 | |
| α-helix | 1024-1040 | 17 | |
| α-helix | 1041-1043 | 3 | |
Chain D: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 842-865 | 24 | |
| α-helix | 879-890 | 12 | |
| α-helix | 892-914 | 23 | |
| α-helix | 919-922 | 4 | |
| α-helix | 930-962 | 33 | |
| α-helix | 965-969 | 5 | |
| α-helix | 973-975 | 3 | |
| α-helix | 976-996 | 21 | |
| α-helix | 1000-1019 | 20 | |
| α-helix | 1024-1043 | 20 | |
Chain E: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 463-470 | 8 | |
| α-helix | 488-514 | 27 | |
Chain F: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 463-471 | 9 | |
| α-helix | 489-493 | 5 | |
| α-helix | 495-512 | 18 | |
| α-helix | 513-515 | 3 | |
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 | 73 | Homo sapiens | O75143 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>8SRM_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
>8SRM_2 Serine/threonine-protein kinase ULK1 (chains C, D)
MEQEHTEILRGLRFTLLFVQHVLEIAALKGSASEAAGGPEYQLQESVVADQISLLSREWG
FAEQLVLYLKVAELLSSGLQSAIDQIRAGKLCLSSTVKQVVRRLNELYKASVVSCQGLSL
RLQRFFLDKQRLLDRIHSITAERLIFSHAVQMVQSAALDEMFQHREGCVPRYHKALLLLE
GLQHMLSDQADIENVTKCKLCIERRLSALLTGICA
Sequence of entity 3 (E, F), FASTA
>8SRM_3 Autophagy-related protein 13 (chains E, F)
KPAFSKDDILPMDLGTFYREFQNPPQLSSLSIDIGAQSMAEDLDSLPEKLAVHEKNVREF
DAFVETLQGSDEA
Primary citation
Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex. Chen, M., Ren, X., Cook, A. et al. bioRxiv. 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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