5X6V: Human heteroheptameric complex
Crystal structure of human heteroheptameric complex. Determined by X-ray diffraction at 2.02 Å resolution. Released 6 Dec 2017.
- Method
- X-ray diffraction
- Resolution
- 2.02 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 7
- Atoms
- 6,417
- Mol. weight
- 92.67 kDa
- Released
- 6 Dec 2017
Explore 5X6V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5X6V contains 31 α-helices and 32 β-strands across 7 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, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-10 | 8 | |
| 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 | 100-121 | 22 | |
Chain B: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 2 |
| α-helix | 4-12 | 9 | |
| β-strand | 19-25 | 7 | 1 |
| β-strand | 31-36 | 6 | 1 |
| α-helix | 42-63 | 22 | |
| α-helix | 67-68 | 2 | |
| β-strand | 69-76 | 8 | 1 |
| β-strand | 79-86 | 8 | 1 |
| β-strand | 89-95 | 7 | 1 |
| α-helix | 101-123 | 23 | |
Chain C: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| β-strand | 18-24 | 7 | 3 |
| β-strand | 30-35 | 6 | 3 |
| α-helix | 39-41 | 3 | |
| α-helix | 42-53 | 12 | |
| β-strand | 64-68 | 5 | 3 |
| β-strand | 72-79 | 8 | 3 |
| β-strand | 82-89 | 8 | 3 |
Chain D: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-11 | 3 | |
| β-strand | 15-22 | 8 | 3 |
| β-strand | 25-31 | 7 | 3 |
| α-helix | 37-51 | 15 | |
| β-strand | 65-69 | 5 | 3 |
| β-strand | 73-80 | 8 | 3 |
| β-strand | 83-90 | 8 | 3 |
Chain E: 8 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-64 | 15 | |
| α-helix | 78-95 | 18 | |
| α-helix | 105-110 | 6 | |
| α-helix | 115-120 | 6 | |
| α-helix | 122-125 | 4 | |
| α-helix | 126-142 | 17 | |
| α-helix | 143-145 | 3 | |
| α-helix | 148-150 | 3 | |
| β-strand | 155 | 1 | 2 |
Chain F: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 188-198 | 11 | |
| β-strand | 202-207 | 6 | 4 |
| β-strand | 213-218 | 6 | 4 |
| α-helix | 227-243 | 17 | |
| β-strand | 249-256 | 8 | 4 |
| β-strand | 259-264 | 6 | 4 |
| β-strand | 270-276 | 7 | 4 |
| α-helix | 283-304 | 22 | |
Chain G: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 239-253 | 15 | |
| β-strand | 257-262 | 6 | 4 |
| β-strand | 268-271 | 4 | 4 |
| α-helix | 275-276 | 2 | |
| α-helix | 278-298 | 21 | |
| β-strand | 314-319 | 6 | 4 |
| β-strand | 323-329 | 7 | 4 |
| β-strand | 334-341 | 8 | 4 |
| α-helix | 344-347 | 4 | |
| α-helix | 348-368 | 21 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ragulator complex protein LAMTOR3 | A | protein | 127 | Homo sapiens | Q9UHA4 (AlphaFold model) |
| Ragulator complex protein LAMTOR2 | B | protein | 125 | Homo sapiens | Q9Y2Q5 (AlphaFold model) |
| Ragulator complex protein LAMTOR5 | C | protein | 91 | Homo sapiens | O43504 (AlphaFold model) |
| Ragulator complex protein LAMTOR4 | D | protein | 99 | Homo sapiens | Q0VGL1 (AlphaFold model) |
| Ragulator complex protein LAMTOR1 | E | protein | 123 | Homo sapiens | Q6IAA8 |
| Ras-related GTP-binding protein A | F | protein | 135 | Homo sapiens | Q7L523 |
| Ras-related GTP-binding protein C | G | protein | 139 | Mus musculus | Q99K70 |
Sequence of entity 1 (A), FASTA
>5X6V_1 Ragulator complex protein LAMTOR3 (chains A)
MGSSADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALAT
DQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEEL
RQVVEVS
Sequence of entity 2 (B), FASTA
>5X6V_2 Ragulator complex protein LAMTOR2 (chains B)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS
Sequence of entity 3 (C), FASTA
>5X6V_3 Ragulator complex protein LAMTOR5 (chains C)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS
Sequence of entity 4 (D), FASTA
>5X6V_4 Ragulator complex protein LAMTOR4 (chains D)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV
Sequence of entity 5 (E), FASTA
>5X6V_5 Ragulator complex protein LAMTOR1 (chains E)
GAASLPSARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSD
LTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQF
GIP
Sequence of entity 6 (F), FASTA
>5X6V_6 Ras-related GTP-binding protein A (chains F)
MADLNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQF
KLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFE
KLERVDGPKHSLLMR
Sequence of entity 7 (G), FASTA
>5X6V_7 Ras-related GTP-binding protein C (chains G)
MQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSC
IYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFH
CFRKAIHEVFEVGVTSHRS
Primary citation
Structural basis for the assembly of the Ragulator-Rag GTPase complex. Yonehara, R., Nada, S., Nakai, T. et al. Nat Commun (2017) 8:1625-1625. DOI 10.1038/s41467-017-01762-3 · 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
- 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
- 5YK3 3.01 Å, human Ragulator complex
- 6U62 3.18 Å, Raptor-Rag-Ragulator complex
Browse structure collections
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