9ED6: CryoEM map of the mLST8-Rag-Ragultor subcomplex

CryoEM map of the mLST8-Rag-Ragultor subcomplex. Determined by electron microscopy at 3.98 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 3.98 Å
Organism: Homo sapiens
Chains: 8
Atoms: 11,246
Mol. weight: 183.09 kDa
Ligands: GTP, MG, GDP
Released: 10 Sept 2025

Explore 9ED6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ED6 contains 48 α-helices and 77 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 B: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	1
α-helix	20-27	8
α-helix	33-36	4
β-strand	46-52	7	1
β-strand	56-62	7	1
α-helix	66-69	4
α-helix	78-82	5
β-strand	87-93	7	1
α-helix	99-116	18
β-strand	121-127	7	1
α-helix	130-132	3
α-helix	137-151	15
β-strand	157-161	5	1
α-helix	168-178	11
α-helix	184-198	15
β-strand	202-206	5	2
β-strand	215-218	4	2
α-helix	227-242	16
α-helix	247-248	2
β-strand	249-255	7	2
β-strand	260-262	3	2
β-strand	265	1	2
β-strand	271-276	6	2
α-helix	283-292	10
α-helix	294-301	8

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	63-67	5	14
α-helix	74-78	5
α-helix	79-83	5
β-strand	111-114	4	14
α-helix	132-136	5
β-strand	139-145	7	14
α-helix	151-167	17
β-strand	172-178	7	14
α-helix	185-204	20
β-strand	213-217	5	14
α-helix	224-234	11
α-helix	240-254	15
β-strand	258-263	6	2
β-strand	268-272	5	2
α-helix	279-299	21
β-strand	315-320	6	2
β-strand	324-330	7	2
β-strand	335-342	8	2
α-helix	343-348	6
α-helix	349-366	18

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48-64	17
α-helix	78-94	17
β-strand	112	1	5
α-helix	116-120	5
α-helix	121-125	5
α-helix	126-142	17
β-strand	155	1	3

Chain E: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	3
α-helix	4-12	9
β-strand	19	1	4
β-strand	23-26	4	4
β-strand	31	1	4
α-helix	42-45	4
α-helix	48-63	16
β-strand	69-75	7	4
β-strand	80-86	7	4
β-strand	89-95	7	4
α-helix	101-109	9
α-helix	112-123	12

Chain F: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	13-15	3
β-strand	19-26	8	4
β-strand	31	1	4
β-strand	35-36	2	4
α-helix	42-45	4
α-helix	47-60	14
β-strand	70-75	6	4
β-strand	78-84	7	4
β-strand	88-95	8	4
α-helix	100-109	10
α-helix	111-119	9

Chain G: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	18	1	5
α-helix	22-24	3
α-helix	37-48	12
α-helix	49-51	3
β-strand	65-70	6	5
β-strand	73-80	8	5
β-strand	83-89	7	5

Chain H: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
β-strand	18-25	8	5
β-strand	30-34	5	5
α-helix	39-41	3
α-helix	43-52	10
α-helix	59-61	3
β-strand	64-69	6	5
β-strand	72-78	7	5
β-strand	82-88	7	5

Chain I: 1 helix, 31 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	6
β-strand	19	1	7
β-strand	23-27	5	6
β-strand	34-39	6	6
β-strand	49-50	2	8
β-strand	56-61	6	8
β-strand	64-69	6	8
β-strand	82	1	8
β-strand	88-93	6	9
β-strand	99-104	6	9
β-strand	108-113	6	9
β-strand	124-126	3	9
β-strand	131-136	6	10
β-strand	142-147	6	10
α-helix	151	1
β-strand	152-156	5	10
β-strand	163-165	3	10
β-strand	173-178	6	11
β-strand	184-189	6	11
β-strand	194-199	6	11
β-strand	210-216	7	11
β-strand	223-228	6	12
β-strand	234-239	6	12
β-strand	243-248	6	12
β-strand	254-259	6	12
β-strand	273-278	6	13
β-strand	284-289	6	13
β-strand	294-298	5	13
β-strand	304	1	13
β-strand	308	1	13
β-strand	315	1	7
β-strand	319-321	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related GTP-binding protein A	B	protein	313	Homo sapiens	Q7L523 (AlphaFold model)
Ragulator complex protein LAMTOR2	E	protein	125	Homo sapiens	Q9Y2Q5 (AlphaFold model)
Ragulator complex protein LAMTOR3	F	protein	124	Homo sapiens	Q9UHA4 (AlphaFold model)
Ragulator complex protein LAMTOR5	H	protein	91	Homo sapiens	O43504 (AlphaFold model)
Target of rapamycin complex subunit LST8	I	protein	326	Homo sapiens	Q9BVC4
Ras-related GTP-binding protein C	C	protein	399	Homo sapiens	Q9HB90
Ragulator complex protein LAMTOR1	D	protein	161	Homo sapiens	Q6IAA8
Ragulator complex protein LAMTOR4	G	protein	99	Homo sapiens	Q0VGL1

Sequence of entity 1 (B), FASTA

>9ED6_1 Ras-related GTP-binding protein A (chains B)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGLDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR

Sequence of entity 2 (E), FASTA

>9ED6_2 Ragulator complex protein LAMTOR2 (chains E)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS

Sequence of entity 3 (F), FASTA

>9ED6_3 Ragulator complex protein LAMTOR3 (chains F)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS

Sequence of entity 4 (H), FASTA

>9ED6_4 Ragulator complex protein LAMTOR5 (chains H)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Sequence of entity 5 (I), FASTA

>9ED6_5 Target of rapamycin complex subunit LST8 (chains I)
MNTSPGTVGSDPVILATAGYDHTVRFWQAHSGICTRTVQHQDSQVNALEVTPDRSMIAAA
GYQHIRMYDLNSNNPNPIISYDGVNKNIASVGFHEDGRWMYTGGEDCTARIWDLRSRNLQ
CQRIFQVNAPINCVCLHPNQAELIVGDQSGAIHIWDLKTDHNEQLIPEPEVSITSAHIDP
DASYMAAVNSTGNCYVWNLTGGIGDEVTQLIPKTKIPAHTRYALQCRFSPDSTLLATCSA
DQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVE
TGEIKREYGGHQKAVVCLAFNDSVLG

Sequence of entity 6 (C), FASTA

>9ED6_6 Ras-related GTP-binding protein C (chains C)
MSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSS
KPRILLMGLRRSGKNSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQ
MDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKV
DGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQL
PTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYG
LKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFR
KAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Sequence of entity 7 (D), FASTA

>9ED6_7 Ragulator complex protein LAMTOR1 (chains D)
MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAK
TASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLA
SEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 8 (G), FASTA

>9ED6_8 Ragulator complex protein LAMTOR4 (chains G)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Structural basis for mTORC1 activation on the lysosomal membrane. Cui, Z., Esposito, A., Napolitano, G. et al. Nature (2025) 647:536-543. DOI 10.1038/s41586-025-09545-3 · PubMed

Other PDB entries of the same protein (UniProt Q7L523 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5X6V 2.02 Å, Crystal structure of human heteroheptameric complex
6S6D 2.5 Å, Crystal structure of RagA-Q66L-GTP/RagC-S75N-GDP GTPase heterodimer complex
6S6A 2.63 Å, Crystal structure of RagA-Q66L/RagC-T90N GTPase heterodimer complex
6EHR 2.9 Å, The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex
7UX2 2.9 Å, cryo-EM structure of the Raptor-TFEB-Rag-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
9ED4 3.23 Å, A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane
6ULG 3.31 Å, Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex
8DHB 3.53 Å, Active FLCN GAP complex

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