6B9X: Ragulator

Crystal structure of Ragulator. Determined by X-ray diffraction at 1.42 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Homo sapiens
Chains: 5
Atoms: 3,997
Mol. weight: 73.92 kDa
Released: 8 Nov 2017

Explore 6B9X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B9X contains 21 α-helices and 22 β-strands across 5 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	98-102	5
α-helix	115-120	6
α-helix	122-125	4
α-helix	126-142	17
α-helix	143-145	3
β-strand	155	1	1

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	4-12	9
β-strand	19-25	7	2
β-strand	31-36	6	2
α-helix	42-60	19
β-strand	71-76	6	2
β-strand	79-86	8	2
β-strand	89-95	7	2
α-helix	101-122	22

Chain C: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
α-helix	13-15	3
β-strand	19-25	7	2
β-strand	31-36	6	2
α-helix	42-45	4
α-helix	47-50	4
α-helix	52-60	9
β-strand	68-74	7	2
β-strand	78-85	8	2
β-strand	88-95	8	2
α-helix	100-119	20

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
β-strand	15-22	8	3
β-strand	25-31	7	3
α-helix	37-52	16
β-strand	65-69	5	3
β-strand	73-80	8	3
β-strand	83-90	8	3

Chain E: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	85-95	11
β-strand	100-106	7	3
β-strand	112-117	6	3
α-helix	121-123	3
α-helix	124-134	11
α-helix	135-137	3
α-helix	144-145	2
β-strand	146-151	6	3
β-strand	154-161	8	3
β-strand	164-170	7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ragulator complex protein LAMTOR1	A	protein	161	Homo sapiens	Q6IAA8 (AlphaFold model)
Ragulator complex protein LAMTOR2	B	protein	126	Homo sapiens	Q9Y2Q5 (AlphaFold model)
Ragulator complex protein LAMTOR3	C	protein	124	Homo sapiens	Q9UHA4 (AlphaFold model)
Ragulator complex protein LAMTOR4	D	protein	99	Homo sapiens	Q0VGL1 (AlphaFold model)
Hepatitis B virus x interacting protein	E	protein	173	Homo sapiens	O43504

Sequence of entity 1 (A), FASTA

>6B9X_1 Ragulator complex protein LAMTOR1 (chains A)
MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAK
TASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLA
SEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 2 (B), FASTA

>6B9X_2 Ragulator complex protein LAMTOR2 (chains B)
AMLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRN
GNQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPL
TQVAAS

Sequence of entity 3 (C), FASTA

>6B9X_3 Ragulator complex protein LAMTOR3 (chains C)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS

Sequence of entity 4 (D), FASTA

>6B9X_4 Ragulator complex protein LAMTOR4 (chains D)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 5 (E), FASTA

>6B9X_5 Hepatitis B virus x interacting protein (chains E)
MEPGAGHLDGHRAGSPSLRQALCDGSAVMFSSKERGRCTVINFVPLEAPLRSTPRSRQVT
EACGGEGRAVPLGSEPEWSVGGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLS
DEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Primary citation

Hybrid Structure of the RagA/C-Ragulator mTORC1 Activation Complex. Su, M.Y., Morris, K.L., Kim, D.J. et al. Mol Cell (2017) 68:835-846.e3. DOI 10.1016/j.molcel.2017.10.016 · PubMed

Other PDB entries of the same protein (UniProt Q6IAA8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
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

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