9ED8: Intermediate state of mTOR on membrane

Intermediate state of mTOR on membrane. Determined by electron microscopy at 3.61 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 3.61 Å
Organism: Homo sapiens
Chains: 3
Atoms: 22,106
Mol. weight: 347.42 kDa
Ligands: MG, GSP, IHP, ANP
Released: 10 Sept 2025

Explore 9ED8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ED8 contains 143 α-helices and 50 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: 137 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	16-30	15
α-helix	34-46	13
α-helix	47-51	5
α-helix	57-75	19
α-helix	80-93	14
α-helix	101-112	12
α-helix	120-134	15
α-helix	141-157	17
α-helix	162-178	17
α-helix	180-198	19
α-helix	203-223	21
α-helix	233-245	13
α-helix	249-251	3
α-helix	257-275	19
α-helix	277-291	15
α-helix	360-381	22
α-helix	386-402	17
α-helix	404-410	7
α-helix	412-423	12
α-helix	427-443	17
α-helix	447-451	5
α-helix	452-462	11
α-helix	464-465	2
α-helix	480-511	32
α-helix	515-527	13
α-helix	529-546	18
α-helix	579-591	13
α-helix	598-609	12
α-helix	616-638	23
α-helix	641-643	3
α-helix	646-665	20
α-helix	669-677	9
α-helix	681-687	7
α-helix	690-700	11
α-helix	705-718	14
α-helix	723-743	21
α-helix	747-763	17
α-helix	765-768	4
α-helix	772-784	13
α-helix	788-789	2
α-helix	793-813	21
α-helix	814-816	3
α-helix	817-829	13
α-helix	837-851	15
α-helix	856-860	5
α-helix	863-874	12
α-helix	878-891	14
α-helix	896-903	8
α-helix	932-940	9
α-helix	943-960	18
α-helix	965-981	17
α-helix	986-989	4
α-helix	990-1003	14
α-helix	1006-1023	18
α-helix	1024-1027	4
α-helix	1028-1041	14
α-helix	1046-1062	17
α-helix	1071-1084	14
α-helix	1089-1100	12
α-helix	1104-1107	4
α-helix	1111-1123	13
α-helix	1129-1142	14
α-helix	1153-1163	11
α-helix	1167-1190	24
α-helix	1192-1202	11
α-helix	1207-1213	7
α-helix	1257-1260	4
α-helix	1262-1268	7
α-helix	1277-1294	18
α-helix	1298-1309	12
α-helix	1311-1316	6
α-helix	1318-1327	10
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	1426-1440	15
α-helix	1444-1446	3
α-helix	1447-1453	7
α-helix	1456-1469	14
α-helix	1474-1487	14
α-helix	1490-1503	14
α-helix	1506-1523	18
α-helix	1526-1535	10
α-helix	1541-1553	13
α-helix	1557-1578	22
α-helix	1583-1607	25
α-helix	1612-1624	13
α-helix	1630-1640	11
α-helix	1646-1649	4
α-helix	1650-1662	13
α-helix	1666-1677	12
α-helix	1681-1684	4
α-helix	1694-1706	13
α-helix	1710-1730	21
α-helix	1734-1762	29
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	1933-1936	4
α-helix	1939-1944	6
α-helix	1951-1967	17
α-helix	1969-1981	13
α-helix	1985-2020	36
α-helix	2023-2035	13
α-helix	2036-2041	6
α-helix	2044-2059	16
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	1	3
β-strand	2159-2162	4	1
β-strand	2170-2175	6	1
β-strand	2176	1	3
β-strand	2181-2188	8	1
α-helix	2192-2211	20
α-helix	2213-2218	6
α-helix	2221-2223	3
β-strand	2227-2229	3	1
β-strand	2234-2238	5	1
α-helix	2239-2240	2
β-strand	2243-2245	3	4
α-helix	2246-2257	12
α-helix	2263-2271	9
α-helix	2275-2277	3
α-helix	2280-2293	14
α-helix	2298-2306	9
α-helix	2310-2334	25
β-strand	2344-2347	4	4
β-strand	2353-2355	3	4
α-helix	2364-2366	3
α-helix	2381-2385	5
α-helix	2392-2396	5
α-helix	2397-2409	13
α-helix	2411-2422	12
α-helix	2491-2509	19
α-helix	2521-2533	13
α-helix	2535-2539	5
α-helix	2543-2545	3

Chain B: 0 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	14-19	6	5
β-strand	23-27	5	5
β-strand	34-39	6	5
β-strand	48-50	3	6
β-strand	56-60	5	6
β-strand	62	1	7
β-strand	65-69	5	6
β-strand	79-81	3	6
β-strand	87	1	7
β-strand	88-93	6	8
β-strand	99-104	6	8
β-strand	108-113	6	8
β-strand	124-126	3	8
β-strand	131-136	6	9
β-strand	142-147	6	9
β-strand	152-156	5	9
β-strand	162-165	4	9
β-strand	177-178	2	10
β-strand	184-188	5	10
β-strand	194-199	6	10
β-strand	210-216	7	10
β-strand	227-228	2	11
β-strand	234-239	6	11
β-strand	243-248	6	11
β-strand	254	1	11
β-strand	258-259	2	11
β-strand	276-278	3	12
β-strand	284-289	6	12
β-strand	293-298	6	12
β-strand	303-307	5	12
β-strand	315-321	7	5

Chain L: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	13
α-helix	18-27	10
β-strand	40-49	10	13
β-strand	52-61	10	13
α-helix	62-64	3
α-helix	69-71	3
β-strand	81-86	6	13
α-helix	90-106	17
β-strand	114-119	6	13
α-helix	131-141	11
β-strand	144-147	4	13
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

>9ED8_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

>9ED8_2 Target of rapamycin complex subunit LST8 (chains B)
MNTSPGTVGSDPVILATAGYDHTVRFWQAHSGICTRTVQHQDSQVNALEVTPDRSMIAAA
GYQHIRMYDLNSNNPNPIISYDGVNKNIASVGFHEDGRWMYTGGEDCTARIWDLRSRNLQ
CQRIFQVNAPINCVCLHPNQAELIVGDQSGAIHIWDLKTDHNEQLIPEPEVSITSAHIDP
DASYMAAVNSTGNCYVWNLTGGIGDEVTQLIPKTKIPAHTRYALQCRFSPDSTLLATCSA
DQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVE
TGEIKREYGGHQKAVVCLAFNDSVLG

Sequence of entity 3 (L), FASTA

>9ED8_3 GTP-binding protein Rheb (chains L)
MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVD
TAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNK
KDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKMDGAASQGKSS
CSVM

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GSP	5'-guanosine-diphosphate-monothiophosphate	C10 H16 N5 O13 P3 S	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
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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