9ED7: Active state of mTOR on membrane

Active state of mTOR on membrane. Determined by electron microscopy at 3.16 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 3.16 Å
Organism: Homo sapiens
Chains: 3
Atoms: 22,412
Mol. weight: 347.47 kDa
Ligands: IHP, GSP, MG, ANP
Released: 10 Sept 2025

Explore 9ED7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ED7 contains 157 α-helices and 46 β-strands across 3 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: 150 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	16-29	14
α-helix	34-50	17
α-helix	57-76	20
α-helix	80-93	14
α-helix	101-114	14
α-helix	120-135	16
α-helix	141-156	16
α-helix	162-178	17
α-helix	180-184	5
α-helix	187-198	12
α-helix	203-222	20
α-helix	233-245	13
α-helix	248-251	4
α-helix	257-275	19
α-helix	277-303	27
α-helix	360-368	9
α-helix	370-380	11
α-helix	386-402	17
α-helix	404-410	7
α-helix	413-423	11
α-helix	430-443	14
α-helix	452-462	11
α-helix	480-493	14
α-helix	495-497	3
α-helix	498-511	14
α-helix	515-527	13
α-helix	529-531	3
α-helix	532-546	15
α-helix	579-591	13
α-helix	599-605	7
α-helix	606-610	5
α-helix	616-629	14
α-helix	631-638	8
α-helix	641-643	3
α-helix	646-665	20
α-helix	669-678	10
α-helix	681-683	3
α-helix	684-687	4
α-helix	690-699	10
α-helix	705-719	15
α-helix	723-743	21
α-helix	747-763	17
α-helix	765-768	4
α-helix	769-771	3
α-helix	772-783	12
α-helix	793-808	16
α-helix	814-816	3
α-helix	817-829	13
α-helix	837-851	15
α-helix	856-860	5
α-helix	862-874	13
α-helix	878-891	14
α-helix	896-903	8
α-helix	908-911	4
α-helix	931-938	8
α-helix	943-960	18
α-helix	962-967	6
α-helix	968-982	15
α-helix	983-989	7
α-helix	990-1003	14
α-helix	1006-1023	18
α-helix	1024-1030	7
α-helix	1031-1039	9
α-helix	1046-1062	17
α-helix	1066-1073	8
α-helix	1075-1083	9
α-helix	1088-1090	3
α-helix	1091-1100	10
α-helix	1104-1107	4
α-helix	1111-1123	13
α-helix	1129-1143	15
α-helix	1151-1155	5
α-helix	1156-1165	10
α-helix	1170-1184	15
α-helix	1186-1189	4
α-helix	1192-1202	11
α-helix	1207-1211	5
α-helix	1262-1268	7
α-helix	1271-1273	3
α-helix	1277-1293	17
α-helix	1298-1302	5
α-helix	1304-1309	6
α-helix	1311-1316	6
α-helix	1318-1326	9
α-helix	1331-1347	17
α-helix	1351-1366	16
α-helix	1380-1389	10
α-helix	1393-1406	14
α-helix	1410-1422	13
α-helix	1426-1439	14
α-helix	1444-1446	3
α-helix	1447-1452	6
α-helix	1456-1467	12
α-helix	1474-1487	14
α-helix	1490-1500	11
α-helix	1506-1523	18
α-helix	1526-1533	8
α-helix	1541-1553	13
α-helix	1557-1579	23
α-helix	1583-1607	25
α-helix	1609-1611	3
α-helix	1612-1625	14
α-helix	1630-1640	11
α-helix	1646-1649	4
α-helix	1650-1661	12
α-helix	1666-1677	12
α-helix	1681-1683	3
α-helix	1688-1690	3
α-helix	1694-1706	13
α-helix	1710-1730	21
α-helix	1737-1762	26
α-helix	1768-1782	15
α-helix	1787-1812	26
α-helix	1870-1895	26
α-helix	1900-1913	14
α-helix	1917-1929	13
α-helix	1932-1938	7
α-helix	1939-1944	6
α-helix	1951-1967	17
α-helix	1969-1980	12
α-helix	1985-2020	36
α-helix	2023-2036	14
α-helix	2037-2041	5
α-helix	2044-2060	17
α-helix	2065-2070	6
α-helix	2071-2075	5
α-helix	2076-2091	16
α-helix	2094-2114	21
α-helix	2115-2117	3
β-strand	2120-2122	3	1
α-helix	2123-2126	4
α-helix	2128-2132	5
β-strand	2139	1	2
α-helix	2140	1
β-strand	2152	1	2
β-strand	2153-2156	4	1
β-strand	2159-2162	4	1
β-strand	2170-2176	7	1
β-strand	2181-2187	7	1
α-helix	2192-2211	20
α-helix	2213-2217	5
α-helix	2221-2223	3
β-strand	2227-2229	3	1
β-strand	2235-2238	4	1
β-strand	2243-2245	3	3
α-helix	2246-2256	11
α-helix	2263-2271	9
α-helix	2275-2277	3
α-helix	2280-2292	13
α-helix	2298-2305	8
α-helix	2310-2334	25
α-helix	2341-2343	3
β-strand	2344-2347	4	3
β-strand	2353-2355	3	3
α-helix	2381-2386	6
α-helix	2395-2409	15
α-helix	2411-2422	12
α-helix	2425-2428	4
α-helix	2491-2509	19
α-helix	2521-2533	13
α-helix	2535-2539	5
α-helix	2543-2545	3

Chain B: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	14-19	6	4
β-strand	23-27	5	4
β-strand	37-39	3	4
β-strand	45-50	6	5
β-strand	56-69	14	5
β-strand	79-87	9	5
β-strand	88-93	6	6
β-strand	99-104	6	6
β-strand	108-113	6	6
β-strand	123-126	4	6
β-strand	131-136	6	7
β-strand	142-147	6	7
β-strand	152-156	5	7
β-strand	162-165	4	7
β-strand	173-178	6	8
β-strand	184-189	6	8
β-strand	194-198	5	8
β-strand	211-212	2	8
β-strand	216	1	8
β-strand	223-228	6	9
β-strand	234-239	6	9
β-strand	243-248	6	9
β-strand	257-259	3	9
α-helix	265-267	3
β-strand	273-277	5	10
β-strand	284-289	6	10
β-strand	293-298	6	10
β-strand	304-308	5	10
β-strand	315-321	7	4

Chain L: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	11
α-helix	19-28	10
β-strand	40-49	10	11
β-strand	52-61	10	11
α-helix	62-63	2
α-helix	72-75	4
β-strand	81-86	6	11
α-helix	90-106	17
β-strand	114-119	6	11
α-helix	131-141	11
β-strand	144-148	5	11
α-helix	153-172	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase mTOR	A	protein	2549	Homo sapiens	P42345 (AlphaFold model)
Target of rapamycin complex subunit LST8	B	protein	326	Homo sapiens	Q9BVC4 (AlphaFold model)
GTP-binding protein Rheb	L	protein	184	Homo sapiens	Q15382 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9ED7_1 Serine/threonine-protein kinase mTOR (chains A)
MLGTGPAAATTAATTSSNVSVLQQFASGLKSRNEETRAKAAKELQHYVTMELREMSQEES
TRFYDQLNHHIFELVSSSDANERKGGILAIASLIGVEGGNATRIGRFANYLRNLLPSNDP
VVMEMASKAIGRLAMAGDTFTAEYVEFEVKRALEWLGADRNEGRRHAAVLVLRELAISVP
TFFFQQVQPFFDNIFVAVWDPKQAIREGAVAALRACLILTTQREPKEMQKPQWYRHTFEE
AEKGFDETLAKEKGMNRDDRIHGALLILNELVRISSMEGERLREEMEEITQQQLVHDKYC
KDLMGFGTKPRHITPFTSFQAVQPQQSNALVGLLGYSSHQGLMGFGTSPSPAKSTLVESR
CCRDLMEEKFDQVCQWVLKCRNSKNSLIQMTILNLLPRLAAFRPSAFTDTQYLQDTMNHV
LSCVKKEKERTAAFQALGLLSVAVRSEFKVYLPRVLDIIRAALPPKDFAHKRQKAMQVDA
TVFTCISMLARAMGPGIQQDIKELLEPMLAVGLSPALTAVLYDLSRQIPQLKKDIQDGLL
KMLSLVLMHKPLRHPGMPKGLAHQLASPGLTTLPEASDVGSITLALRTLGSFEFEGHSLT
QFVRHCADHFLNSEHKEIRMEAARTCSRLLTPSIHLISGHAHVVSQTAVQVVADVLSKLL
VVGITDPDPDIRYCVLASLDERFDAHLAQAENLQALFVALNDQVFEIRELAICTVGRLSS
MNPAFVMPFLRKMLIQILTELEHSGIGRIKEQSARMLGHLVSNAPRLIRPYMEPILKALI
LKLKDPDPDPNPGVINNVLATIGELAQVSGLEMRKWVDELFIIIMDMLQDSSLLAKRQVA
LWTLGQLVASTGYVVEPYRKYPTLLEVLLNFLKTEQNQGTRREAIRVLGLLGALDPYKHK
VNIGMIDQSRDASAVSLSESKSSQDSSDYSTSEMLVNMGNLPLDEFYPAVSMVALMRIFR
DQSLSHHHTMVVQAITFIFKSLGLKCVQFLPQVMPTFLNVIRVCDGAIREFLFQQLGMLV
SFVKSHIRPYMDEIVTLMREFWVMNTSIQSTIILLIEQIVVALGGEFKLYLPQLIPHMLR
VFMHDNSPGRIVSIKLLAAIQLFGANLDDYLHLLLPPIVKLFDAPEAPLPSRKAALETVD
RLTESLDFTDYASRIIHPIVRTLDQSPELRSTAMDTLSSLVFQLGKKYQIFIPMVNKVLV
RHRINHQRYDVLICRIVKGYTLADEEEDPLIYQHRMLRSGQGDALASGPVETGPMKKLHV
STINLQKAWGAARRVSKDDWLEWLRRLSLELLKDSSSPSLRSCWALAQAYNPMARDLFNA
AFVSCWSELNEDQQDELIRSIELALTSQDIAEVTQTLLNLAEFMEHSDKGPLPLRDDNGI
VLLGERAAKCRAYAKALHYKELEFQKGPTPAILESLISINNKLQQPEAAAGVLEYAMKHF
GELEIQATWYEKLHEWEDALVAYDKKMDTNKDDPELMLGRMRCLEALGEWGQLHQQCCEK
WTLVNDETQAKMARMAAAAAWGLGQWDSMEEYTCMIPRDTHDGAFYRAVLALHQDLFSLA
QQCIDKARDLLDAELTAMAGESYSRAYGAMVSCHMLSELEEVIQYKLVPERREIIRQIWW
ERLQGCQRIVEDWQKILMVRSLVVSPHEDMRTWLKYASLCGKSGRLALAHKTLVLLLGVD
PSRQLDHPLPTVHPQVTYAYMKNMWKSARKIDAFQHMQHFVQTMQQQAQHAIATEDQQHK
QELHKLMARCFLKLGEWQLNLQGINESTIPKVLQYYSAATEHDRSWYKAWHAWAVMNFEA
VLHYKHQNQARDEKKKLRHASGANITNATTAATTAATATTTASTEGSNSESEAESTENSP
TPSPLQKKVTEDLSKTLLMYTVPAVQGFFRSISLSRGNNLQDTLRVLTLWFDYGHWPDVN
EALVEGVKAIQIDTWLQVIPQLIARIDTPRPLVGRLIHQLLTDIGRYHPQALIYPLTVAS
KSTTTARHNAANKILKNMCEHSNTLVQQAMMVSEELIRVAILWHEMWHEGLEEASRLYFG
ERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVKDLTQA
WDLYYHVFRRISKQLPQLTSLELQYVSPKLLMCRDLELAVPGTYDPNQPIIRIQSIAPSL
QVITSKQRPRKLTLMGSNGHEFVFLLKGHEDLRQDERVMQLFGLVNTLLANDPTSLRKNL
SIQRYAVIPLSTNSGLIGWVPHCDTLHALIRDYREKKKILLNIEHRIMLRMAPDYDHLTL
MQKVEVFEHAVNNTAGDDLAKLLWLKSPSSEVWFDRRTNYTRSLAVMSMVGYILGLGDRH
PSNLMLDRLSGKILHIDFGDCFEVAMTREKFPEKIPFRLTRMLTNAMEVTGLDGNYRITC
HTVMEVLREHKDSVMAVLEAFVYDPLLNWRLMDTNTKGNKRSRTRTDSYSAGQSVEILDG
VELGEPAHKKTGTTVPESIHSFIGDGLVKPEALNKKAIQIINRVRDKLTGRDFSHDDTLD
VPTQVELLIKQATSHENLCQCYIGWCPFW

Sequence of entity 2 (B), FASTA

>9ED7_2 Target of rapamycin complex subunit LST8 (chains B)
MNTSPGTVGSDPVILATAGYDHTVRFWQAHSGICTRTVQHQDSQVNALEVTPDRSMIAAA
GYQHIRMYDLNSNNPNPIISYDGVNKNIASVGFHEDGRWMYTGGEDCTARIWDLRSRNLQ
CQRIFQVNAPINCVCLHPNQAELIVGDQSGAIHIWDLKTDHNEQLIPEPEVSITSAHIDP
DASYMAAVNSTGNCYVWNLTGGIGDEVTQLIPKTKIPAHTRYALQCRFSPDSTLLATCSA
DQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVE
TGEIKREYGGHQKAVVCLAFNDSVLG

Sequence of entity 3 (L), FASTA

>9ED7_3 GTP-binding protein Rheb (chains L)
MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVD
TAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNK
KDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKMDGAASQGKSS
CSVM

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
GSP	5'-guanosine-diphosphate-monothiophosphate	C10 H16 N5 O13 P3 S	1
MG	Magnesium ion	Mg	3
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	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 P42345 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4DRI 1.45 Å, Co-crystal structure of the PPIase domain of FKBP51, Rapamycin and the FRB fragment of…
9DBO 1.55 Å, Crystal structure of a synthetic Fab (R3E9) in complex with the FRB domain of mTOR
5GPG 1.67 Å, Co-crystal structure of the FK506 binding domain of human FKBP25, Rapamycin and the FRB…
5WBH 1.75 Å, Structure of the FRB domain of mTOR bound to a substrate recruitment peptide of S6K1
4DRJ 1.8 Å, o-crystal structure of the PPIase domain of FKBP52, Rapamycin and the FRB fragment of mTOR
3FAP 1.85 Å, Atomic structures of the rapamycin analogs in complex with both human FKBP12 and frb…
8PPZ 1.85 Å, Co-crystal structure of FKBP12, compound 7 and the FRB fragment of mTOR
8XI9 1.85 Å, Crystal structure of FRB-FKBP fusion protein in complex with rapamycin
9PIW 1.9 Å, Crystal structure of a synthetic Fab (1A) in complex with the FRB domain of mTOR
9DL0 2.0 Å, Crystal structure of a synthetic Fab (R3H8) in complex with the FRB domain of mTOR
9PJ1 2.05 Å, Crystal structure of a synthetic Fab (4R) in complex with the ternary assembly of…
9PIU 2.18 Å, Crystal structure of a synthetic Fab (2C) in complex with the FRB domain of mTOR

Browse structure collections

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