6WJ2: Ragulator complex protein LAMTOR1

CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state. Determined by electron microscopy at 3.2 Å resolution. Released 2 Sept 2020.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,909
Mol. weight: 173.28 kDa
Ligands: GDP, L8S, MG
Released: 2 Sept 2020

Explore 6WJ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WJ2 contains 40 α-helices and 46 β-strands across 8 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	50-64	15
α-helix	84-96	13
α-helix	105-108	4
α-helix	115-118	4
α-helix	122-125	4
α-helix	127-143	17
β-strand	155-156	2	1

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-2	2	1
α-helix	4-12	9
β-strand	17	1	2
β-strand	19-25	7	2
β-strand	31-36	6	2
α-helix	44-58	15
β-strand	69-76	8	2
β-strand	79-84	6	2
β-strand	90-96	7	2
α-helix	103-122	20

Chain C: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	13-15	3
β-strand	19-25	7	2
β-strand	35-36	2	2
α-helix	49-59	11
β-strand	68-75	8	2
β-strand	78-86	9	2
β-strand	88-95	8	2
α-helix	100-109	10
α-helix	111-120	10

Chain D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	15-22	8	3
β-strand	25-26	2	3
α-helix	31-33	3
α-helix	37-50	14
β-strand	65-69	5	3
β-strand	74-80	7	3
β-strand	83-89	7	3

Chain E: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	85-94	10
β-strand	100-106	7	3
β-strand	112-116	5	3
α-helix	124-137	14
β-strand	146-148	3	3
β-strand	156-160	5	3
β-strand	165-170	6	3

Chain F: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	4
α-helix	22-28	7
β-strand	51-52	2	5
β-strand	56-57	2	5
β-strand	58-61	4	4
α-helix	68-78	11
β-strand	85-93	9	4
α-helix	100-115	16
β-strand	123-127	5	4
α-helix	137-151	15
β-strand	159-161	3	4
α-helix	168-178	11
α-helix	185-198	14
β-strand	202-207	6	6
β-strand	215-217	3	6
α-helix	228-242	15
α-helix	243-245	3
β-strand	249-255	7	6
β-strand	260-267	8	6
β-strand	270-276	7	6
α-helix	284-300	17

Chain G: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	63-67	5	7
α-helix	77-82	6
α-helix	87-90	4
β-strand	100-103	4	7
β-strand	113-116	4	7
α-helix	117-118	2
α-helix	131-134	4
β-strand	139-145	7	7
α-helix	151-167	17
β-strand	172-178	7	7
α-helix	185-204	20
β-strand	214-217	4	7
α-helix	224-234	11
α-helix	240-254	15
β-strand	258-263	6	6
β-strand	272	1	6
α-helix	281-299	19
β-strand	315-320	6	6
β-strand	325-330	6	6
β-strand	335-341	7	6
α-helix	349-368	20

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	61-72	12
α-helix	90-91	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ragulator complex protein LAMTOR1	A	protein	166	Homo sapiens	Q6IAA8 (AlphaFold model)
Ragulator complex protein LAMTOR2	B	protein	127	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)
Ragulator complex protein LAMTOR5	E	protein	173	Homo sapiens	O43504
Ras-related GTP-binding protein A	F	protein	336	Homo sapiens	Q7L523
Ras-related GTP-binding protein C	G	protein	404	Homo sapiens	Q9HB90
Sodium-coupled neutral amino acid transporter 9	H	protein	122	Homo sapiens	Q8NBW4

Sequence of entity 1 (A), FASTA

>6WJ2_1 Ragulator complex protein LAMTOR1 (chains A)
SNAEFMACCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLS
SILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQP
HQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 2 (B), FASTA

>6WJ2_2 Ragulator complex protein LAMTOR2 (chains B)
GAMLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDR
NGNQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEP
LTQVAAS

Sequence of entity 3 (C), FASTA

>6WJ2_3 Ragulator complex protein LAMTOR3 (chains C)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS

Sequence of entity 4 (D), FASTA

>6WJ2_4 Ragulator complex protein LAMTOR4 (chains D)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 5 (E), FASTA

>6WJ2_5 Ragulator complex protein LAMTOR5 (chains E)
MEPGAGHLDGHRAGSPSLRQALCDGSAVMFSSKERGRCTVINFVPLEAPLRSTPRSRQVT
EACGGEGRAVPLGSEPEWSVGGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLS
DEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Sequence of entity 6 (F), FASTA

>6WJ2_6 Ras-related GTP-binding protein A (chains F)
MSWSHPQFEKGGFDIDYKDDDDKMPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTR
RLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESR
ELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLEC
ACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHY
QCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMS
DPSIPSAATLINIRNARKHFEKLERVDGPKHSLLMR

Sequence of entity 7 (G), FASTA

>6WJ2_7 Ras-related GTP-binding protein C (chains G)
GADSRMSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPG
GADSSKPRILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIW
DFPGQMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEV
FIHKVNGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQK
LIPQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDV
SCIYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYN
FHCFRKAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Sequence of entity 8 (H), FASTA

>6WJ2_8 Sodium-coupled neutral amino acid transporter 9 (chains H)
GGTMANMNSDSRHLGTSEVDHERDPGPMNIQFEPSDLRSKRPFCIEPTNIVNVNHVIQRV
SDHASAMNKRIHYYSRLTTPADKALIAPDHVVPAPEECYVYSPLGSAYKLQSYTEGYGKN
TS

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
L8S	9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-al…	C10 H15 N4 O14 P3 S	1
MG	Magnesium ion	Mg	1

Primary citation

Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9. Fromm, S.A., Lawrence, R.E., Hurley, J.H. Nat Struct Mol Biol (2020) 27:1017-1023. DOI 10.1038/s41594-020-0490-9 · 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
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
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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