5YK3: Human Ragulator complex
human Ragulator complex. Determined by X-ray diffraction at 3.01 Å resolution. Released 23 Jan 2019.
- Method
- X-ray diffraction
- Resolution
- 3.01 Å
- Organism
- Homo sapiens
- Chains
- 15
- Atoms
- 11,608
- Mol. weight
- 169.17 kDa
- Released
- 23 Jan 2019
Explore 5YK3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5YK3 contains 61 α-helices and 64 β-strands across 15 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: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 79-98 | 20 | |
| α-helix | 105-110 | 6 | |
| α-helix | 115-120 | 6 | |
| α-helix | 123-125 | 3 | |
| α-helix | 126-144 | 19 | |
Chain B: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-12 | 8 | |
| β-strand | 19-25 | 7 | 4 |
| β-strand | 31-35 | 5 | 4 |
| α-helix | 42-57 | 16 | |
| β-strand | 69-76 | 8 | 4 |
| β-strand | 79-86 | 8 | 4 |
| β-strand | 89-95 | 7 | 4 |
| α-helix | 101-115 | 15 | |
Chain C: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-10 | 9 | |
| α-helix | 13-15 | 3 | |
| β-strand | 19-25 | 7 | 4 |
| β-strand | 31-36 | 6 | 4 |
| α-helix | 42-45 | 4 | |
| α-helix | 47-50 | 4 | |
| α-helix | 52-60 | 9 | |
| β-strand | 68-75 | 8 | 4 |
| β-strand | 78-85 | 8 | 4 |
| β-strand | 88-95 | 8 | 4 |
| α-helix | 100-115 | 16 | |
| α-helix | 118-121 | 4 | |
Chain D: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-10 | 8 | |
| β-strand | 17-22 | 6 | 5 |
| β-strand | 26-30 | 5 | 5 |
| α-helix | 38-51 | 14 | |
| α-helix | 54-56 | 3 | |
| β-strand | 65-69 | 5 | 5 |
| β-strand | 73-80 | 8 | 5 |
| β-strand | 83-90 | 8 | 5 |
Chain E: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-13 | 10 | |
| β-strand | 18-24 | 7 | 5 |
| β-strand | 30-35 | 6 | 5 |
| α-helix | 39-41 | 3 | |
| α-helix | 42-52 | 11 | |
| α-helix | 53-55 | 3 | |
| β-strand | 64-68 | 5 | 5 |
| β-strand | 72-79 | 8 | 5 |
| β-strand | 82-89 | 8 | 5 |
Chain F: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 80-98 | 19 | |
| α-helix | 105-109 | 5 | |
| α-helix | 115-120 | 6 | |
| α-helix | 122-125 | 4 | |
| α-helix | 126-143 | 18 | |
Chain G: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-12 | 7 | |
| β-strand | 19-25 | 7 | 6 |
| β-strand | 31-35 | 5 | 6 |
| α-helix | 42-57 | 16 | |
| β-strand | 69-76 | 8 | 6 |
| β-strand | 80-86 | 7 | 6 |
| β-strand | 89-95 | 7 | 6 |
| α-helix | 101-120 | 20 | |
Chain H: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-12 | 11 | |
| α-helix | 13-15 | 3 | |
| β-strand | 19-25 | 7 | 6 |
| β-strand | 31-36 | 6 | 6 |
| α-helix | 42-45 | 4 | |
| α-helix | 47-50 | 4 | |
| α-helix | 52-60 | 9 | |
| β-strand | 68-75 | 8 | 6 |
| β-strand | 78-85 | 8 | 6 |
| β-strand | 88-95 | 8 | 6 |
| α-helix | 100-121 | 22 | |
7 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 LAMTOR3 | H, m | protein | 124 | Homo sapiens | Q9UHA4 (AlphaFold model) |
| Ragulator complex protein LAMTOR2 | G, l | protein | 125 | Homo sapiens | Q9Y2Q5 (AlphaFold model) |
| Ragulator complex protein LAMTOR5 | o | protein | 90 | Homo sapiens | O43504 (AlphaFold model) |
| Ragulator complex protein LAMTOR4 | n | protein | 88 | Homo sapiens | Q0VGL1 (AlphaFold model) |
| Ragulator complex protein LAMTOR1 | k | protein | 85 | Homo sapiens | Q6IAA8 |
| Ragulator complex protein LAMTOR3 | C | protein | 123 | Homo sapiens | Q9UHA4 (AlphaFold model) |
| Ragulator complex protein LAMTOR2 | B | protein | 125 | Homo sapiens | Q9Y2Q5 (AlphaFold model) |
| Ragulator complex protein LAMTOR5 | E, J | protein | 91 | Homo sapiens | O43504 (AlphaFold model) |
| Ragulator complex protein LAMTOR4 | D | protein | 96 | Homo sapiens | Q0VGL1 (AlphaFold model) |
| Ragulator complex protein LAMTOR1 | A, F | protein | 85 | Homo sapiens | Q6IAA8 |
| Ragulator complex protein LAMTOR4 | I | protein | 99 | Homo sapiens | Q0VGL1 (AlphaFold model) |
Sequence of entity 1 (H, m), FASTA
>5YK3_1 Ragulator complex protein LAMTOR3 (chains H, m)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS
Sequence of entity 2 (G, l), FASTA
>5YK3_2 Ragulator complex protein LAMTOR2 (chains G, l)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS
Sequence of entity 3 (o), FASTA
>5YK3_3 Ragulator complex protein LAMTOR5 (chains o)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMA
Sequence of entity 4 (n), FASTA
>5YK3_4 Ragulator complex protein LAMTOR4 (chains n)
ATAGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMNVPFK
RLSVVFGEHTLLVTVSGQRVFVVKRQNR
Sequence of entity 5 (k), FASTA
>5YK3_5 Ragulator complex protein LAMTOR1 (chains k)
AAHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIA
AYAYSALSQIRVDAKEELVVQFGIP
Sequence of entity 6 (C), FASTA
>5YK3_6 Ragulator complex protein LAMTOR3 (chains C)
AADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEV
Sequence of entity 7 (B), FASTA
>5YK3_7 Ragulator complex protein LAMTOR2 (chains B)
AAAPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QAAAA
Sequence of entity 8 (E, J), FASTA
>5YK3_8 Ragulator complex protein LAMTOR5 (chains E, J)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS
Sequence of entity 9 (D), FASTA
>5YK3_9 Ragulator complex protein LAMTOR4 (chains D)
ATALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMNV
PFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPI
Sequence of entity 10 (A, F), FASTA
>5YK3_10 Ragulator complex protein LAMTOR1 (chains A, F)
AQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIA
AYAYSALSQIRVDAKEELVVQFGIP
Sequence of entity 11 (I), FASTA
>5YK3_11 Ragulator complex protein LAMTOR4 (chains I)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV
Primary citation
Structural insight into the Ragulator complex which anchors mTORC1 to the lysosomal membrane. Mu, Z., Wang, L., Deng, W. et al. Cell Discov (2017) 3:17049-17049. DOI 10.1038/celldisc.2017.49 · PubMed
Other PDB entries of the same protein (UniProt Q9UHA4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6B9X 1.42 Å, Crystal structure of Ragulator
- 3CPT 1.9 Å, MP1-p14 Scaffolding complex
- 1SKO 2.0 Å, MP1-p14 Complex
- 2ZL1 2.0 Å, MP1-p14 Scaffolding complex
- 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
- 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
- 6U62 3.18 Å, Raptor-Rag-Ragulator complex
Browse structure collections
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