5Y3A: Ragulator complex
Crystal structure of Ragulator complex (p18 49-161). Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Dec 2017.
- Method
- X-ray diffraction
- Resolution
- 2.9 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 7,463
- Mol. weight
- 121.71 kDa
- Released
- 27 Dec 2017
Explore 5Y3A in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5Y3A contains 43 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: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 78-96 | 19 | |
| α-helix | 105-109 | 5 | |
| β-strand | 112 | 1 | 1 |
| α-helix | 115-120 | 6 | |
| α-helix | 122-125 | 4 | |
| α-helix | 126-141 | 16 | |
| α-helix | 142-145 | 4 | |
Chain B: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-13 | 7 | |
| β-strand | 19-25 | 7 | 2 |
| β-strand | 31-36 | 6 | 2 |
| α-helix | 42-63 | 22 | |
| β-strand | 71-76 | 6 | 2 |
| β-strand | 79-86 | 8 | 2 |
| β-strand | 89-95 | 7 | 2 |
| α-helix | 101-115 | 15 | |
Chain C: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| α-helix | 13-15 | 3 | |
| β-strand | 19-26 | 8 | 2 |
| β-strand | 31-36 | 6 | 2 |
| α-helix | 47-50 | 4 | |
| α-helix | 52-60 | 9 | |
| α-helix | 61-63 | 3 | |
| β-strand | 68-74 | 7 | 2 |
| β-strand | 78-85 | 8 | 2 |
| β-strand | 88-95 | 8 | 2 |
| α-helix | 100-117 | 18 | |
| α-helix | 118-120 | 3 | |
Chain D: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-10 | 8 | |
| β-strand | 15-22 | 8 | 1 |
| β-strand | 26-31 | 6 | 1 |
| α-helix | 37-51 | 15 | |
| β-strand | 65-69 | 5 | 1 |
| β-strand | 73-80 | 8 | 1 |
| β-strand | 83-90 | 8 | 1 |
Chain E: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 85-95 | 11 | |
| β-strand | 100-106 | 7 | 1 |
| β-strand | 112-117 | 6 | 1 |
| α-helix | 121-123 | 3 | |
| α-helix | 124-135 | 12 | |
| β-strand | 146-152 | 7 | 1 |
| β-strand | 154-160 | 7 | 1 |
| β-strand | 165-170 | 6 | 1 |
Chain F: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 82-96 | 15 | |
| α-helix | 105-110 | 6 | |
| α-helix | 115-120 | 6 | |
| α-helix | 122-125 | 4 | |
| α-helix | 126-141 | 16 | |
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 | 42-61 | 20 | |
| β-strand | 69-76 | 8 | 3 |
| β-strand | 80-86 | 7 | 3 |
| β-strand | 89-95 | 7 | 3 |
| α-helix | 101-115 | 15 | |
| α-helix | 117-119 | 3 | |
Chain H: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-11 | 8 | |
| 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 | |
| α-helix | 61-63 | 3 | |
| β-strand | 68-75 | 8 | 3 |
| β-strand | 78-85 | 8 | 3 |
| β-strand | 88-95 | 8 | 3 |
| α-helix | 100-109 | 10 | |
| α-helix | 111-121 | 11 | |
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 | 112 | Homo sapiens | Q6IAA8 (AlphaFold model) |
| Ragulator complex protein LAMTOR2 | B, G | protein | 127 | 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 | 93 | Homo sapiens | O43504 |
Sequence of entity 1 (A, F), FASTA
>5Y3A_1 Ragulator complex protein LAMTOR1 (chains A, F)
EQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLP
SLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP
Sequence of entity 2 (B, G), FASTA
>5Y3A_2 Ragulator complex protein LAMTOR2 (chains B, G)
MAMLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDR
NGNQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEP
LTQVAAS
Sequence of entity 3 (C, H), FASTA
>5Y3A_3 Ragulator complex protein LAMTOR3 (chains C, H)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS
Sequence of entity 4 (D, I), FASTA
>5Y3A_4 Ragulator complex protein LAMTOR4 (chains D, I)
MGMTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRG
MNVPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV
Sequence of entity 5 (E, J), FASTA
>5Y3A_5 Ragulator complex protein LAMTOR5 (chains E, J)
MAMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSD
PTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS
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
- 5Y39 2.65 Å, Crystal structure of Ragulator complex (p18 76-145)
- 6EHR 2.9 Å, The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex
- 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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