5Y39: Ragulator complex
Crystal structure of Ragulator complex (p18 76-145). Determined by X-ray diffraction at 2.65 Å resolution. Released 6 Dec 2017.
- Method
- X-ray diffraction
- Resolution
- 2.65 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 6,808
- Mol. weight
- 111.2 kDa
- Released
- 6 Dec 2017
Explore 5Y39 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5Y39 contains 40 α-helices and 41 β-strands across 10 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: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 82-96 | 15 | |
| α-helix | 115-120 | 6 | |
| α-helix | 123-125 | 3 | |
| α-helix | 126-144 | 19 | |
Chain B: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-12 | 6 | |
| β-strand | 19-25 | 7 | 1 |
| β-strand | 31-36 | 6 | 1 |
| α-helix | 42-61 | 20 | |
| β-strand | 69-76 | 8 | 1 |
| β-strand | 79-86 | 8 | 1 |
| β-strand | 89-95 | 7 | 1 |
| α-helix | 101-116 | 16 | |
| α-helix | 117-119 | 3 | |
Chain C: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| α-helix | 13-15 | 3 | |
| β-strand | 19-25 | 7 | 1 |
| β-strand | 31-36 | 6 | 1 |
| α-helix | 42-44 | 3 | |
| α-helix | 47-50 | 4 | |
| α-helix | 52-60 | 9 | |
| β-strand | 68-75 | 8 | 1 |
| β-strand | 78-85 | 8 | 1 |
| β-strand | 88-95 | 8 | 1 |
| α-helix | 100-115 | 16 | |
| α-helix | 118-120 | 3 | |
Chain D: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-10 | 10 | |
| β-strand | 15-22 | 8 | 2 |
| β-strand | 25-31 | 7 | 2 |
| α-helix | 37-51 | 15 | |
| β-strand | 65-69 | 5 | 2 |
| β-strand | 73-80 | 8 | 2 |
| β-strand | 83-90 | 8 | 2 |
| α-helix | 91 | 1 | |
Chain E: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 85-96 | 12 | |
| β-strand | 100-107 | 8 | 2 |
| β-strand | 112-117 | 6 | 2 |
| α-helix | 121-123 | 3 | |
| α-helix | 124-135 | 12 | |
| α-helix | 144-145 | 2 | |
| β-strand | 146-150 | 5 | 2 |
| β-strand | 154-160 | 7 | 2 |
| β-strand | 164-171 | 8 | 2 |
Chain F: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 115-118 | 4 | |
| α-helix | 123-125 | 3 | |
| α-helix | 126-142 | 17 | |
Chain G: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-12 | 6 | |
| β-strand | 19-26 | 8 | 3 |
| β-strand | 31-36 | 6 | 3 |
| α-helix | 42-58 | 17 | |
| α-helix | 60-63 | 4 | |
| β-strand | 69-76 | 8 | 3 |
| β-strand | 79-86 | 8 | 3 |
| β-strand | 89-95 | 7 | 3 |
| α-helix | 101-121 | 21 | |
Chain H: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| α-helix | 13-15 | 3 | |
| β-strand | 19-25 | 7 | 3 |
| β-strand | 31-36 | 6 | 3 |
| α-helix | 42-45 | 4 | |
| α-helix | 47-50 | 4 | |
| α-helix | 52-60 | 9 | |
| β-strand | 68-75 | 8 | 3 |
| β-strand | 78-85 | 8 | 3 |
| β-strand | 88-95 | 8 | 3 |
| α-helix | 100-115 | 16 | |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ragulator complex protein LAMTOR1 | A, F | protein | 70 | Homo sapiens | Q6IAA8 (AlphaFold model) |
| Ragulator complex protein LAMTOR2 | B, G | protein | 125 | Homo sapiens | Q9Y2Q5 (AlphaFold model) |
| Ragulator complex protein LAMTOR3 | C, H | protein | 124 | Homo sapiens | Q9UHA4 (AlphaFold model) |
| Ragulator complex protein LAMTOR4 | D, I | protein | 101 | Homo sapiens | Q0VGL1 (AlphaFold model) |
| Ragulator complex protein LAMTOR5 | E, J | protein | 90 | Homo sapiens | O43504 |
Sequence of entity 1 (A, F), FASTA
>5Y39_1 Ragulator complex protein LAMTOR1 (chains A, F)
MEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRI
AAYAYSALSQ
Sequence of entity 2 (B, G), FASTA
>5Y39_2 Ragulator complex protein LAMTOR2 (chains B, G)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS
Sequence of entity 3 (C, H), FASTA
>5Y39_3 Ragulator complex protein LAMTOR3 (chains C, H)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS
Sequence of entity 4 (D, I), FASTA
>5Y39_4 Ragulator complex protein LAMTOR4 (chains D, I)
MGMTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRG
MNVPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV
Sequence of entity 5 (E, J), FASTA
>5Y39_5 Ragulator complex protein LAMTOR5 (chains E, J)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMA
Primary citation
Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1. Zhang, T., Wang, R., Wang, Z. et al. Nat Commun (2017) 8:1394-1394. DOI 10.1038/s41467-017-01567-4 · PubMed
Other PDB entries of the same protein (UniProt Q6IAA8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6B9X 1.42 Å, Crystal structure of Ragulator
- 5X6V 2.02 Å, Crystal structure of human heteroheptameric complex
- 6EHP 2.3 Å, The crystal structure of the human LAMTOR complex
- 5X6U 2.4 Å, Crystal structure of human heteropentameric complex
- 6EHR 2.9 Å, The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex
- 5Y3A 2.9 Å, Crystal structure of Ragulator complex (p18 49-161)
- 7UX2 2.9 Å, cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex
- 5YK3 3.01 Å, human Ragulator complex
- 6U62 3.18 Å, Raptor-Rag-Ragulator complex
- 6WJ2 3.2 Å, CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state
- 7UXC 3.2 Å, cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with symmetry expansion
- 7UXH 3.2 Å, cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex
Browse structure collections
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