6U62: Raptor-Rag-Ragulator complex

Raptor-Rag-Ragulator complex. Determined by electron microscopy at 3.18 Å resolution. Released 30 Oct 2019.

Method: Electron microscopy
Resolution: 3.18 Å
Organism: Homo sapiens
Chains: 8
Atoms: 17,036
Mol. weight: 305.71 kDa
Ligands: GTP, GDP, MG
Released: 30 Oct 2019

Explore 6U62 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U62 contains 93 α-helices and 85 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: 50 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	33-36	4
α-helix	41-43	3
β-strand	57-65	9	1
α-helix	85-87	3
α-helix	95-111	17
β-strand	118-123	6	1
α-helix	128-140	13
β-strand	145-152	8	1
β-strand	166-167	2	2
α-helix	169-171	3
β-strand	174-175	2	2
α-helix	179-185	7
β-strand	190-195	6	1
α-helix	200-218	19
β-strand	242-243	2	1
α-helix	262-268	7
α-helix	270-279	10
α-helix	292-295	4
α-helix	310-327	18
α-helix	332-337	6
α-helix	341-356	16
β-strand	366	1	1
α-helix	370-372	3
α-helix	378-391	14
α-helix	393-395	3
α-helix	404-406	3
α-helix	408-422	15
α-helix	433-439	7
α-helix	446-457	12
α-helix	461-470	10
α-helix	473-478	6
α-helix	479-481	3
α-helix	488-499	12
α-helix	503-505	3
α-helix	506-511	6
α-helix	515-523	9
α-helix	532-542	11
α-helix	547-555	9
α-helix	558-563	6
α-helix	571-584	14
α-helix	589-596	8
α-helix	600-603	4
α-helix	605-609	5
α-helix	615-626	12
α-helix	637-648	12
α-helix	649-652	4
α-helix	657-673	17
α-helix	675-688	14
α-helix	689-691	3
α-helix	781-789	9
α-helix	807-819	13
α-helix	824-843	20
α-helix	919-922	4
α-helix	924-926	3
α-helix	959-963	5
α-helix	964-968	5
α-helix	983-1004	22
β-strand	1015-1021	7	3
β-strand	1028-1031	4	4
β-strand	1038-1041	4	4
β-strand	1045-1050	6	4
β-strand	1055-1061	7	4
β-strand	1070-1076	7	5
β-strand	1083-1088	6	5
β-strand	1092-1097	6	5
β-strand	1107-1113	7	5
β-strand	1127-1131	5	6
β-strand	1137-1142	6	6
β-strand	1146-1151	6	6
β-strand	1156-1162	7	6
β-strand	1171-1175	5	7
β-strand	1180-1184	5	7
β-strand	1190-1193	4	7
β-strand	1203-1207	5	7
β-strand	1214-1217	4	8
β-strand	1228-1231	4	8
β-strand	1237-1238	2	8
β-strand	1240	1	9
β-strand	1243	1	9
α-helix	1252-1253	2
β-strand	1258-1261	4	10
β-strand	1268-1271	4	10
β-strand	1277-1280	4	10
β-strand	1286-1290	5	10
β-strand	1304-1309	6	3
β-strand	1316-1320	5	3
β-strand	1324-1329	6	3

Chain B: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	11
α-helix	20-28	9
α-helix	33-38	6
α-helix	39-42	4
β-strand	46-53	8	11
β-strand	56-62	7	11
α-helix	67-71	5
α-helix	78-81	4
β-strand	85-93	9	11
α-helix	101-116	16
β-strand	121-127	7	11
α-helix	129-131	3
α-helix	137-148	12
β-strand	157-161	5	11
α-helix	168-176	9
α-helix	177-179	3
α-helix	184-197	14
β-strand	202-207	6	12
β-strand	213-218	6	12
α-helix	227-243	17
β-strand	249-254	6	12
β-strand	260-267	8	12
β-strand	270-276	7	12
α-helix	283-292	10
α-helix	294-297	4
α-helix	298-300	3

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	63-68	6	13
α-helix	74-81	8
β-strand	111-114	4	13
α-helix	133-136	4
β-strand	139-145	7	13
α-helix	153-167	15
β-strand	172-178	7	13
α-helix	180-182	3
α-helix	185-204	20
β-strand	213-217	5	13
α-helix	224-234	11
α-helix	240-254	15
β-strand	258-263	6	12
β-strand	271	1	12
α-helix	279-299	21
β-strand	315-320	6	12
β-strand	324-330	7	12
β-strand	335-342	8	12
α-helix	345-348	4
α-helix	349-366	18

Chain D: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	49-64	16
α-helix	65-67	3
α-helix	78-94	17
α-helix	107-109	3
α-helix	116-119	4
α-helix	129-142	14
α-helix	143-145	3
β-strand	155	1	14

Chain E: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	14
α-helix	4-12	9
β-strand	19-25	7	15
β-strand	31-36	6	15
α-helix	42-61	20
β-strand	69-75	7	15
β-strand	80-85	6	15
β-strand	90-95	6	15
α-helix	101-123	23

Chain F: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	21-26	6	15
β-strand	31-33	3	15
α-helix	43-45	3
α-helix	47-60	14
β-strand	70-75	6	15
β-strand	79-83	5	15
β-strand	85	1	15
β-strand	88-93	6	15
α-helix	100-119	20

Chain G: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	16
β-strand	20	1	16
β-strand	21	1	17
β-strand	26	1	17
α-helix	37-49	13
β-strand	66-69	4	16
β-strand	74-80	7	16
β-strand	83-86	4	16
β-strand	89	1	16

Chain H: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	10
β-strand	18-24	7	18
β-strand	30-35	6	18
α-helix	39-41	3
α-helix	45-53	9
β-strand	64	1	16
β-strand	65-69	5	18
β-strand	72-76	5	18
β-strand	85-88	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulatory-associated protein of mTOR	A	protein	1392	Homo sapiens	Q8N122 (AlphaFold model)
Ras-related GTP-binding protein A	B	protein	313	Homo sapiens	Q7L523 (AlphaFold model)
Ras-related GTP-binding protein C	C	protein	400	Homo sapiens	Q9HB90 (AlphaFold model)
Ragulator complex protein LAMTOR1	D	protein	158	Homo sapiens	Q6IAA8 (AlphaFold model)
Ragulator complex protein LAMTOR2	E	protein	125	Homo sapiens	Q9Y2Q5
Ragulator complex protein LAMTOR3	F	protein	162	Homo sapiens	Q9UHA4
Ragulator complex protein LAMTOR4	G	protein	100	Homo sapiens	Q0VGL1
Ragulator complex protein LAMTOR5	H	protein	91	Homo sapiens	O43504

Sequence of entity 1 (A), FASTA

>6U62_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
NDYYISVYSVEKRVRGGGSLEVLFQGPGSGGGSDYKDDDDKSSGWSHPQFEKGGGARGGS
GGGSWSHPQFEK

Sequence of entity 2 (B), FASTA

>6U62_2 Ras-related GTP-binding protein A (chains B)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR

Sequence of entity 3 (C), FASTA

>6U62_3 Ras-related GTP-binding protein C (chains C)
GPSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADS
SKPRILLMGLRRSGKNSIQKVVFHKMSPNENLFLESTNKIYKDDISNSSFVNFQIWDFPG
QMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHK
VDGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQ
LPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIY
GLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCF
RKAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Sequence of entity 4 (D), FASTA

>6U62_4 Ragulator complex protein LAMTOR1 (chains D)
GPSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAKTAS
NIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEP
IPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQFGIP

Sequence of entity 5 (E), FASTA

>6U62_5 Ragulator complex protein LAMTOR2 (chains E)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS

Sequence of entity 6 (F), FASTA

>6U62_6 Ragulator complex protein LAMTOR3 (chains F)
MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQG
SKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQV
VEVSENLYFQGSSGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 7 (G), FASTA

>6U62_7 Ragulator complex protein LAMTOR4 (chains G)
GPTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGM
NVPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 8 (H), FASTA

>6U62_8 Ragulator complex protein LAMTOR5 (chains H)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Ligands and cofactors

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

Primary citation

Structural basis for the docking of mTORC1 on the lysosomal surface. Rogala, K.B., Gu, X., Kedir, J.F. et al. Science (2019) 366:468-475. DOI 10.1126/science.aay0166 · 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
7UX2 2.9 Å, cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex
8RCN 3.1 Å, CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458…
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

Browse structure collections

About this viewer

MolViewer shows 6U62 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.