6WJ3: Ragulator complex protein LAMTOR1

CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the post-GAP state. Determined by electron microscopy at 3.9 Å resolution. Released 2 Sept 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,912
Mol. weight: 173.16 kDa
Ligands: GDP, U3J
Released: 2 Sept 2020

Explore 6WJ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WJ3 contains 44 α-helices and 51 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	115-118	4
α-helix	123-124	2
α-helix	127-143	17
α-helix	148-150	3
β-strand	155-156	2	1

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	1-2	2	1
α-helix	4-12	9
β-strand	21-25	5	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: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	13-15	3
β-strand	21-25	5	2
β-strand	31	1	2
β-strand	35-36	2	2
α-helix	42-44	3
α-helix	47-60	14
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	4-10	7
β-strand	18-22	5	3
β-strand	25-26	2	3
α-helix	31-33	3
α-helix	37-51	15
β-strand	66-69	4	3
β-strand	73-80	8	3
β-strand	83-90	8	3

Chain E: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	85-93	9
β-strand	102-106	5	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	165-169	5	3

Chain F: 10 helices, 15 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	70-78	9
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	168-180	13
α-helix	185-197	13
β-strand	202-204	3	6
β-strand	206	1	7
β-strand	207	1	6
β-strand	213	1	7
α-helix	225-227	3
α-helix	228-242	15
α-helix	243-245	3
β-strand	249	1	8
β-strand	253-256	4	6
β-strand	260-267	8	6
β-strand	270-275	6	6
α-helix	284-300	17

Chain G: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	63-67	5	9
α-helix	77-81	5
α-helix	89-92	4
β-strand	102	1	9
β-strand	113-114	2	9
α-helix	117-118	2
α-helix	131-135	5
β-strand	139-145	7	9
α-helix	151-167	17
β-strand	172-178	7	9
α-helix	185-204	20
β-strand	214-217	4	9
α-helix	224-234	11
α-helix	240-254	15
β-strand	258-263	6	10
α-helix	282-299	18
β-strand	314-316	3	6
β-strand	319	1	10
β-strand	320	1	8
β-strand	325-327	3	10
β-strand	328	1	6
β-strand	335-341	7	10
α-helix	344-346	3
α-helix	349-368	20

Chain H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	61-73	13
α-helix	90-91	2
α-helix	92-94	3

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

>6WJ3_1 Ragulator complex protein LAMTOR1 (chains A)
SNAEFMACCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLS
SILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQP
HQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 2 (B), FASTA

>6WJ3_2 Ragulator complex protein LAMTOR2 (chains B)
GAMLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDR
NGNQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEP
LTQVAAS

Sequence of entity 3 (C), FASTA

>6WJ3_3 Ragulator complex protein LAMTOR3 (chains C)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS

Sequence of entity 4 (D), FASTA

>6WJ3_4 Ragulator complex protein LAMTOR4 (chains D)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 5 (E), FASTA

>6WJ3_5 Ragulator complex protein LAMTOR5 (chains E)
MEPGAGHLDGHRAGSPSLRQALCDGSAVMFSSKERGRCTVINFVPLEAPLRSTPRSRQVT
EACGGEGRAVPLGSEPEWSVGGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLS
DEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Sequence of entity 6 (F), FASTA

>6WJ3_6 Ras-related GTP-binding protein A (chains F)
MSWSHPQFEKGGFDIDYKDDDDKMPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTR
RLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESR
ELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLEC
ACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHY
QCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMS
DPSIPSAATLINIRNARKHFEKLERVDGPKHSLLMR

Sequence of entity 7 (G), FASTA

>6WJ3_7 Ras-related GTP-binding protein C (chains G)
GADSRMSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPG
GADSSKPRILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIW
DFPGQMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEV
FIHKVNGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQK
LIPQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDV
SCIYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYN
FHCFRKAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Sequence of entity 8 (H), FASTA

>6WJ3_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
U3J	xanthosine diphosphate	C10 H14 N4 O12 P2	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
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

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