7UX2: Raptor-TFEB-Rag-Ragulator complex

cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex. Determined by electron microscopy at 2.9 Å resolution. Released 30 Nov 2022.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 16
Atoms: 27,249
Mol. weight: 496.49 kDa
Ligands: GTP, MG, GDP
Released: 30 Nov 2022

Explore 7UX2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UX2 contains 148 α-helices and 130 β-strands across 16 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: 51 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	27-28	2
α-helix	33-36	4
α-helix	41-43	3
β-strand	57-64	8	1
β-strand	85	1	2
β-strand	88	1	2
α-helix	90-92	3
α-helix	95-113	19
β-strand	118-123	6	1
α-helix	127-140	14
β-strand	145-151	7	1
α-helix	156-159	4
β-strand	163-166	4	3
β-strand	173-174	2	4
β-strand	175-178	4	3
α-helix	179-185	7
β-strand	190-195	6	1
α-helix	199-217	19
β-strand	241-244	4	1
α-helix	250-253	4
α-helix	262-268	7
α-helix	270-281	12
α-helix	294-297	4
α-helix	308-327	20
α-helix	330-337	8
α-helix	341-358	18
β-strand	365-366	2	1
α-helix	370-372	3
α-helix	378-391	14
α-helix	393-394	2
α-helix	395-399	5
α-helix	403-406	4
α-helix	408-422	15
α-helix	423-425	3
α-helix	433-438	6
α-helix	446-457	12
α-helix	461-470	10
α-helix	472-479	8
α-helix	487-499	13
α-helix	503-505	3
α-helix	506-511	6
α-helix	515-523	9
α-helix	532-543	12
α-helix	547-555	9
α-helix	558-564	7
α-helix	571-584	14
α-helix	589-597	9
α-helix	600-604	5
α-helix	606-609	4
α-helix	613-625	13
α-helix	628-629	2
α-helix	635-648	14
α-helix	649-651	3
α-helix	657-673	17
α-helix	675-689	15
α-helix	781-788	8
β-strand	802	1	5
β-strand	805	1	5
α-helix	807-819	13
α-helix	824-842	19
α-helix	924-926	3
α-helix	959-964	6
α-helix	965-968	4
α-helix	982-1007	26
β-strand	1015-1021	7	6
β-strand	1028-1031	4	7
β-strand	1038-1041	4	7
β-strand	1045-1049	5	7
β-strand	1058-1061	4	7
β-strand	1070-1076	7	8
β-strand	1083-1088	6	8
β-strand	1092-1097	6	8
β-strand	1107-1113	7	8
β-strand	1127-1132	6	9
β-strand	1137-1142	6	9
β-strand	1146-1151	6	9
β-strand	1156-1162	7	9
β-strand	1169-1175	7	10
β-strand	1180-1185	6	10
β-strand	1190-1193	4	10
β-strand	1203-1207	5	10
β-strand	1214-1216	3	11
β-strand	1219-1220	2	12
β-strand	1226-1229	4	12
β-strand	1230-1231	2	11
β-strand	1235-1239	5	12
β-strand	1246-1251	6	12
β-strand	1256-1261	6	13
β-strand	1267-1272	6	13
β-strand	1277-1281	5	13
β-strand	1285-1290	6	13
β-strand	1304-1309	6	6
β-strand	1316-1320	5	6
β-strand	1324-1329	6	6

Chain B: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	14
α-helix	20-29	10
α-helix	33-38	6
α-helix	39-42	4
β-strand	46-53	8	14
β-strand	56-62	7	14
α-helix	67-71	5
α-helix	72-76	5
α-helix	78-82	5
β-strand	87-93	7	14
α-helix	101-116	16
α-helix	120	1
β-strand	121-127	7	14
α-helix	134-136	3
α-helix	137-151	15
β-strand	157-161	5	14
α-helix	168-180	13
α-helix	184-198	15
β-strand	203-207	5	15
β-strand	215-217	3	15
α-helix	227-242	16
α-helix	243-245	3
β-strand	249-255	7	15
β-strand	260-265	6	15
β-strand	270-274	5	15
α-helix	283-298	16

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	63-68	6	16
α-helix	74-78	5
α-helix	79-83	5
β-strand	111-114	4	16
β-strand	139-145	7	16
α-helix	151-167	17
β-strand	172-178	7	16
α-helix	185-205	21
β-strand	213-217	5	16
α-helix	224-234	11
α-helix	240-254	15
β-strand	258-263	6	15
β-strand	268-272	5	15
α-helix	276-278	3
α-helix	279-299	21
β-strand	315-320	6	15
β-strand	324-330	7	15
β-strand	335-342	8	15
α-helix	345-348	4
α-helix	349-367	19

Chain D: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	48-64	17
α-helix	66-67	2
α-helix	78-98	21
α-helix	105-109	5
α-helix	115-119	5
α-helix	122-125	4
α-helix	128-143	16
β-strand	155	1	17

Chain E: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	17
α-helix	4-12	9
β-strand	21-25	5	18
β-strand	31-36	6	18
α-helix	42-63	22
β-strand	69-76	8	18
β-strand	79-85	7	18
β-strand	90-95	6	18
α-helix	101-123	23

Chain F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	21-26	6	18
β-strand	31-36	6	18
α-helix	42-45	4
α-helix	47-50	4
α-helix	52-60	9
β-strand	68-75	8	18
β-strand	79-84	6	18
β-strand	88-93	6	18
α-helix	100-121	22

Chain G: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	17-22	6	19
β-strand	25	1	19
α-helix	38-50	13
β-strand	66-69	4	19
β-strand	73-80	8	19
β-strand	83-90	8	19

Chain H: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	18-24	7	19
β-strand	30-34	5	19
α-helix	39-41	3
α-helix	43-50	8
β-strand	64-68	5	19
β-strand	73-76	4	19
β-strand	85-88	4	19

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulatory-associated protein of mTOR	A	protein	1335	Homo sapiens	Q8N122 (AlphaFold model)
Ras-related GTP-binding protein A	B, I	protein	313	Homo sapiens	Q7L523 (AlphaFold model)
Ras-related GTP-binding protein C	C, J	protein	399	Homo sapiens	Q9HB90 (AlphaFold model)
Ragulator complex protein LAMTOR1	D, K	protein	161	Homo sapiens	Q6IAA8 (AlphaFold model)
Ragulator complex protein LAMTOR2	E, L	protein	125	Homo sapiens	Q9Y2Q5
Ragulator complex protein LAMTOR3	F, M	protein	124	Homo sapiens	Q9UHA4
Ragulator complex protein LAMTOR4	G, N	protein	99	Homo sapiens	Q0VGL1
Ragulator complex protein LAMTOR5	H, O	protein	91	Homo sapiens	O43504
Transcription factor EB	P	protein	476	Homo sapiens	P19484

Sequence of entity 1 (A), FASTA

>7UX2_1 Regulatory-associated protein of mTOR (chains A)
MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLAQSWRMKDRMKTVSV
ALVLCLNVGVDPPDVVKTTPCARLECWIDPLSMGPQKALETIGANLQKQYENWQPRARYK
QSLDPTVDEVKKLCTSLRRNAKEERVLFHYNGHGVPRPTVNGEVWVFNKNYTQYIPLSIY
DLQTWMGSPSIFVYDCSNAGLIVKSFKQFALQREQELEVAAINPNHPLAQMPLPPSMKNC
IQLAACEATELLPMIPDLPADLFTSCLTTPIKIALRWFCMQKCVSLVPGVTLDLIEKIPG
RLNDRRTPLGELNWIFTAITDTIAWNVLPRDLFQKLFRQDLLVASLFRNFLLAERIMRSY
NCTPVSSPRLPPTYMHAMWQAWDLAVDICLSQLPTIIEEGTAFRHSPFFAEQLTAFQVWL
TMGVENRNPPEQLPIVLQVLLSQVHRLRALDLLGRFLDLGPWAVSLALSVGIFPYVLKLL
QSSARELRPLLVFIWAKILAVDSSCQADLVKDNGHKYFLSVLADPYMPAEHRTMTAFILA
VIVNSYHTGQEACLQGNLIAICLEQLNDPHPLLRQWVAICLGRIWQNFDSARWCGVRDSA
HEKLYSLLSDPIPEVRCAAVFALGTFVGNSAERTDHSTTIDHNVAMMLAQLVSDGSPMVR
KELVVALSHLVVQYESNFCTVALQFIEEEKNYALPSPATTEGGSLTPVRDSPCTPRLRSV
SSYGNIRAVATARSLNKSLQNLSLTEESGGAVAFSPGNLSTSSSASSTLGSPENEEHILS
FETIDKMRRASSYSSLNSLIGVSFNSVYTQIWRVLLHLAADPYPEVSDVAMKVLNSIAYK
ATVNARPQRVLDTSSLTQSAPASPTNKGVHIHQAGGSPPASSTSSSSLTNDVAKQPVSRD
LPSGRPGTTGPAGAQYTPHSHQFPRTRKMFDKGPEQTADDADDAAGHKSFISATVQTGFC
DWSARYFAQPVMKIPEEHDLESQIRKEREWRFLRNSRVRRQAQQVIQKGITRLDDQIFLN
RNPGVPSVVKFHPFTPCIAVADKDSICFWDWEKGEKLDYFHNGNPRYTRVTAMEYLNGQD
CSLLLTATDDGAIRVWKNFADLEKNPEMVTAWQGLSDMLPTTRGAGMVVDWEQETGLLMS
SGDVRIVRIWDTDREMKVQDIPTGADSCVTSLSCDSHRSLIVAGLGDGSIRVYDRRMALS
ECRVMTYREHTAWVVKASLQKRPDGHIVSVSVNGDVRIFDPRMPESVNVLQIVKGLTALD
IHPQADLIACGSVNQFTAIYNSSGELINNIKYYDGFMGQRVGAISCLAFHPHWPHLAVGS
NDYYISVYSVEKRVR

Sequence of entity 2 (B, I), FASTA

>7UX2_2 Ras-related GTP-binding protein A (chains B, I)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGLDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR

Sequence of entity 3 (C, J), FASTA

>7UX2_3 Ras-related GTP-binding protein C (chains C, J)
MSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSS
KPRILLMGLRRSGKNSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQ
MDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKV
DGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQL
PTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYG
LKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFR
KAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Sequence of entity 4 (D, K), FASTA

>7UX2_4 Ragulator complex protein LAMTOR1 (chains D, K)
MGCCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAK
TASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLA
SEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 5 (E, L), FASTA

>7UX2_5 Ragulator complex protein LAMTOR2 (chains E, L)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS

Sequence of entity 6 (F, M), FASTA

>7UX2_6 Ragulator complex protein LAMTOR3 (chains F, M)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVS

Sequence of entity 7 (G, N), FASTA

>7UX2_7 Ragulator complex protein LAMTOR4 (chains G, N)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 8 (H, O), FASTA

>7UX2_8 Ragulator complex protein LAMTOR5 (chains H, O)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Sequence of entity 9 (P), FASTA

>7UX2_9 Transcription factor EB (chains P)
MASRIGLRMQLMREQAQQEEQRERMQQQAVMHYMQQQQQQQQQQLGGPPTPAINTPVHFQ
SPPPVPGEVLKVQSYLENPTSYHLQQSQHQKVREYLSETYGNKFAAHISPAQGSPKPPPA
ASPGVRAGHVLSSSAGNSAPNSPMAMLHIGSNPERELDDVIDNIMRLDDVLGYINPEMQM
PNTLPLSSSHLNVYSSDPQVTASLVGVTSSSCPADLTQKRELTDAESRALAKERQKKDNH
NLIERRRRFNINDRIKELGMLIPKANDLDVRWNKGTILKASVDYIRRMQKDLQKSRELEN
HSRRLEMTNKQLWLRIQELEMQARVHGLPTTSPSGMNMAELAQQVVKQELPSEEGPGEAL
MLGAEVPDPEPLPALPPQAPLPLPTQPPSPFHHLDFSHSLSFGGREDEGPPGYPEPLAPG
HGSPFPSLSKKDLDLMLLDDSLLPLASDPLLSTMSPEASKASSRRSSFSMEEGDVL

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. Cui, Z., Napolitano, G., de Araujo, M.E.G. et al. Nature (2023) 614:572-579. DOI 10.1038/s41586-022-05652-7 · PubMed

Other PDB entries of the same protein (UniProt Q8N122 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ERA 2.86 Å, RMC-5552 in complex with mTORC1 and FKBP12
8RCN 3.1 Å, CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458…
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
6BCX 3.23 Å, mTORC1 structure refined to 3.0 angstroms
9ED4 3.23 Å, A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane
9F42 3.27 Å, cryo-EM structure of LST2 TOS peptide bound to human mTOR complex 1, focused on RAPTOR
8RCK 3.4 Å, CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458…
9F43 3.49 Å, cryo-EM structure of human LST2 bound to human mTOR complex 1, focused on RAPTOR
7PEB 3.67 Å, cryo-EM structure of DEPTOR bound to human mTOR complex 1, focussed on one protomer
9F44 3.68 Å, cryo-EM structure of LST2 TOS peptide bound to human mTOR complex 1

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