9TDT: Serine/threonine-protein kinase mTOR

cryo-EM structure of dephosphorylated mTOR complex 2, focused on a single protomer. Determined by electron microscopy at 3.0 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 25,046
Mol. weight: 584.85 kDa
Ligands: ZN, IHP
Released: 22 Apr 2026

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

Secondary structure: helices and β-sheets

9TDT contains 193 α-helices and 47 β-strands across 4 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: 101 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	799-808	10
α-helix	811-813	3
α-helix	817-824	8
α-helix	837-851	15
α-helix	857-860	4
α-helix	864-874	11
α-helix	878-891	14
α-helix	896-901	6
α-helix	931-934	4
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	1009-1023	15
α-helix	1024-1030	7
α-helix	1031-1041	11
α-helix	1049-1063	15
α-helix	1064-1069	6
α-helix	1071-1084	14
α-helix	1088-1090	3
α-helix	1091-1100	10
α-helix	1104-1109	6
α-helix	1111-1123	13
α-helix	1129-1142	14
α-helix	1149-1151	3
α-helix	1152-1163	12
α-helix	1170-1184	15
α-helix	1185-1191	7
α-helix	1192-1201	10
α-helix	1207-1218	12
α-helix	1229-1237	9
α-helix	1263-1269	7
α-helix	1277-1294	18
α-helix	1298-1301	4
α-helix	1304-1309	6
α-helix	1312-1316	5
α-helix	1318-1326	9
α-helix	1331-1346	16
α-helix	1351-1366	16
α-helix	1376-1379	4
α-helix	1380-1389	10
α-helix	1393-1404	12
α-helix	1410-1422	13
α-helix	1426-1439	14
α-helix	1442-1444	3
α-helix	1447-1452	6
α-helix	1456-1469	14
α-helix	1474-1486	13
α-helix	1490-1498	9
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	1612-1623	12
α-helix	1630-1640	11
α-helix	1650-1662	13
α-helix	1666-1677	12
α-helix	1688-1690	3
α-helix	1694-1705	12
α-helix	1710-1727	18
α-helix	1739-1762	24
α-helix	1768-1782	15
α-helix	1787-1810	24
α-helix	1874-1894	21
α-helix	1900-1913	14
α-helix	1917-1929	13
α-helix	1932-1938	7
α-helix	1939-1943	5
α-helix	1951-1967	17
α-helix	1969-1979	11
α-helix	1985-1998	14
α-helix	2003-2020	18
α-helix	2023-2035	13
α-helix	2036-2041	6
α-helix	2044-2059	16
α-helix	2065-2091	27
α-helix	2094-2114	21
α-helix	2115-2117	3
β-strand	2120-2122	3	1
α-helix	2123-2126	4
α-helix	2128-2131	4
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	2193-2210	18
α-helix	2213-2218	6
β-strand	2227-2231	5	1
β-strand	2234-2238	5	1
β-strand	2243-2245	3	3
α-helix	2246-2257	12
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
β-strand	2344-2347	4	3
β-strand	2353-2355	3	3
α-helix	2364-2366	3
α-helix	2381-2385	5
α-helix	2395-2409	15
α-helix	2411-2422	12
α-helix	2428-2430	3
α-helix	2495-2507	13
α-helix	2521-2533	13
α-helix	2535-2538	4
α-helix	2543-2545	3

Chain C: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	14-19	6	4
β-strand	23-27	5	4
β-strand	34-39	6	4
β-strand	47-50	4	5
β-strand	56-60	5	5
β-strand	65-69	5	5
β-strand	79-82	4	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	161-165	5	7
β-strand	173-178	6	8
β-strand	184-189	6	8
β-strand	194-201	8	8
β-strand	208-216	9	8
β-strand	223-228	6	9
β-strand	234-239	6	9
β-strand	243-248	6	9
β-strand	254-259	6	9
α-helix	265-267	3
β-strand	275-278	4	10
β-strand	284-288	5	10
β-strand	294-298	5	10
β-strand	304-308	5	10
β-strand	315-321	7	4

Chain E: 83 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	34-46	13
α-helix	53-70	18
α-helix	81-91	11
α-helix	97-110	14
α-helix	114-121	8
α-helix	125-134	10
α-helix	140-156	17
α-helix	158-160	3
α-helix	163-175	13
α-helix	184-195	12
α-helix	199-205	7
α-helix	207-217	11
α-helix	221-236	16
α-helix	241-243	3
α-helix	251-254	4
α-helix	255-258	4
α-helix	270-272	3
α-helix	273-291	19
α-helix	295-302	8
α-helix	308-316	9
α-helix	321-334	14
α-helix	337-341	5
α-helix	346-352	7
α-helix	360-362	3
α-helix	368-376	9
α-helix	378-379	2
β-strand	386	1	11
α-helix	387-401	15
α-helix	404-413	10
α-helix	417-437	21
α-helix	440-443	4
α-helix	446-448	3
α-helix	450-457	8
α-helix	463-485	23
α-helix	492-506	15
α-helix	525-535	11
α-helix	537-540	4
α-helix	548-556	9
α-helix	568-581	14
α-helix	583-585	3
β-strand	592	1	12
α-helix	598-614	17
α-helix	616-638	23
α-helix	650-652	3
β-strand	654	1	12
α-helix	655-658	4
α-helix	659-667	9
α-helix	670-678	9
α-helix	681-690	10
α-helix	696-702	7
α-helix	712-723	12
α-helix	726-741	16
α-helix	747-751	5
α-helix	752-757	6
α-helix	758-760	3
α-helix	764-777	14
α-helix	781-790	10
α-helix	795-797	3
α-helix	799-805	7
α-helix	806-810	5
α-helix	812-819	8
α-helix	823-830	8
α-helix	831-835	5
α-helix	836-851	16
β-strand	877	1	11
α-helix	878-880	3
α-helix	882-886	5
α-helix	890-898	9
α-helix	902-910	9
α-helix	917-933	17
α-helix	937-946	10
α-helix	949-958	10
α-helix	962-975	14
α-helix	979-986	8
β-strand	990-992	3	13
α-helix	1002-1005	4
β-strand	1428-1430	3	13
α-helix	1433-1436	4
α-helix	1445-1447	3
α-helix	1481-1484	4
α-helix	1489-1491	3
α-helix	1523-1528	6
α-helix	1531-1535	5
α-helix	1607-1623	17
α-helix	1629-1642	14
α-helix	1644-1646	3
α-helix	1650-1662	13
α-helix	1667-1675	9
α-helix	1683-1693	11

Chain G: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-21	15
α-helix	26-30	5
α-helix	33-35	3
α-helix	85-99	15
β-strand	104-107	4	5
α-helix	120-123	4
α-helix	132-134	3
α-helix	136-138	3
α-helix	139-142	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase mTOR	A	protein	2590	Homo sapiens	P42345 (AlphaFold model)
Target of rapamycin complex subunit LST8	C	protein	326	Homo sapiens	Q9BVC4 (AlphaFold model)
Rapamycin-insensitive companion of mTOR	E	protein	1734	Homo sapiens	Q6R327 (AlphaFold model)
Target of rapamycin complex 2 subunit MAPKAP1	G	protein	522	Homo sapiens	Q9BPZ7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9TDT_1 Serine/threonine-protein kinase mTOR (chains A)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGENLYFQGGTMLGTGPAAATTAATTSSNV
SVLQQFASGLKSRNEETRAKAAKELQHYVTMELREMSQEESTRFYDQLNHHIFELVSSSD
ANERKGGILAIASLIGVEGGNATRIGRFANYLRNLLPSNDPVVMEMASKAIGRLAMAGDT
FTAEYVEFEVKRALEWLGADRNEGRRHAAVLVLRELAISVPTFFFQQVQPFFDNIFVAVW
DPKQAIREGAVAALRACLILTTQREPKEMQKPQWYRHTFEEAEKGFDETLAKEKGMNRDD
RIHGALLILNELVRISSMEGERLREEMEEITQQQLVHDKYCKDLMGFGTKPRHITPFTSF
QAVQPQQSNALVGLLGYSSHQGLMGFGTSPSPAKSTLVESRCCRDLMEEKFDQVCQWVLK
CRNSKNSLIQMTILNLLPRLAAFRPSAFTDTQYLQDTMNHVLSCVKKEKERTAAFQALGL
LSVAVRSEFKVYLPRVLDIIRAALPPKDFAHKRQKAMQVDATVFTCISMLARAMGPGIQQ
DIKELLEPMLAVGLSPALTAVLYDLSRQIPQLKKDIQDGLLKMLSLVLMHKPLRHPGMPK
GLAHQLASPGLTTLPEASDVGSITLALRTLGSFEFEGHSLTQFVRHCADHFLNSEHKEIR
MEAARTCSRLLTPSIHLISGHAHVVSQTAVQVVADVLSKLLVVGITDPDPDIRYCVLASL
DERFDAHLAQAENLQALFVALNDQVFEIRELAICTVGRLSSMNPAFVMPFLRKMLIQILT
ELEHSGIGRIKEQSARMLGHLVSNAPRLIRPYMEPILKALILKLKDPDPDPNPGVINNVL
ATIGELAQVSGLEMRKWVDELFIIIMDMLQDSSLLAKRQVALWTLGQLVASTGYVVEPYR
KYPTLLEVLLNFLKTEQNQGTRREAIRVLGLLGALDPYKHKVNIGMIDQSRDASAVSLSE
SKSSQDSSDYSTSEMLVNMGNLPLDEFYPAVSMVALMRIFRDQSLSHHHTMVVQAITFIF
KSLGLKCVQFLPQVMPTFLNVIRVCDGAIREFLFQQLGMLVSFVKSHIRPYMDEIVTLMR
EFWVMNTSIQSTIILLIEQIVVALGGEFKLYLPQLIPHMLRVFMHDNSPGRIVSIKLLAA
IQLFGANLDDYLHLLLPPIVKLFDAPEAPLPSRKAALETVDRLTESLDFTDYASRIIHPI
VRTLDQSPELRSTAMDTLSSLVFQLGKKYQIFIPMVNKVLVRHRINHQRYDVLICRIVKG
YTLADEEEDPLIYQHRMLRSGQGDALASGPVETGPMKKLHVSTINLQKAWGAARRVSKDD
WLEWLRRLSLELLKDSSSPSLRSCWALAQAYNPMARDLFNAAFVSCWSELNEDQQDELIR
SIELALTSQDIAEVTQTLLNLAEFMEHSDKGPLPLRDDNGIVLLGERAAKCRAYAKALHY
KELEFQKGPTPAILESLISINNKLQQPEAAAGVLEYAMKHFGELEIQATWYEKLHEWEDA
LVAYDKKMDTNKDDPELMLGRMRCLEALGEWGQLHQQCCEKWTLVNDETQAKMARMAAAA
AWGLGQWDSMEEYTCMIPRDTHDGAFYRAVLALHQDLFSLAQQCIDKARDLLDAELTAMA
GESYSRAYGAMVSCHMLSELEEVIQYKLVPERREIIRQIWWERLQGCQRIVEDWQKILMV
RSLVVSPHEDMRTWLKYASLCGKSGRLALAHKTLVLLLGVDPSRQLDHPLPTVHPQVTYA
YMKNMWKSARKIDAFQHMQHFVQTMQQQAQHAIATEDQQHKQELHKLMARCFLKLGEWQL
NLQGINESTIPKVLQYYSAATEHDRSWYKAWHAWAVMNFEAVLHYKHQNQARDEKKKLRH
ASGANITNATTAATTAATATTTASTEGSNSESEAESTENSPTPSPLQKKVTEDLSKTLLM
YTVPAVQGFFRSISLSRGNNLQDTLRVLTLWFDYGHWPDVNEALVEGVKAIQIDTWLQVI
PQLIARIDTPRPLVGRLIHQLLTDIGRYHPQALIYPLTVASKSTTTARHNAANKILKNMC
EHSNTLVQQAMMVSEELIRVAILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMME
RGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSGNVKDLTQAWDLYYHVFRRISKQLPQLT
SLELQYVSPKLLMCRDLELAVPGTYDPNQPIIRIQSIAPSLQVITSKQRPRKLTLMGSNG
HEFVFLLKGHEDLRQDERVMQLFGLVNTLLANDPTSLRKNLSIQRYAVIPLSTNSGLIGW
VPHCDTLHALIRDYREKKKILLNIEHRIMLRMAPDYDHLTLMQKVEVFEHAVNNTAGDDL
AKLLWLKSPSSEVWFDRRTNYTRSLAVMSMVGYILGLGDRHPSNLMLDRLSGKILHIDFG
DCFEVAMTREKFPEKIPFRLTRMLTNAMEVTGLDGNYRITCHTVMEVLREHKDSVMAVLE
AFVYDPLLNWRLMDTNTKGNKRSRTRTDSYSAGQSVEILDGVELGEPAHKKTGTTVPESI
HSFIGDGLVKPEALNKKAIQIINRVRDKLTGRDFSHDDTLDVPTQVELLIKQATSHENLC
QCYIGWCPFW

Sequence of entity 2 (C), FASTA

>9TDT_2 Target of rapamycin complex subunit LST8 (chains C)
MNTSPGTVGSDPVILATAGYDHTVRFWQAHSGICTRTVQHQDSQVNALEVTPDRSMIAAA
GYQHIRMYDLNSNNPNPIISYDGVNKNIASVGFHEDGRWMYTGGEDCTARIWDLRSRNLQ
CQRIFQVNAPINCVCLHPNQAELIVGDQSGAIHIWDLKTDHNEQLIPEPEVSITSAHIDP
DASYMAAVNSTGNCYVWNLTGGIGDEVTQLIPKTKIPAHTRYALQCRFSPDSTLLATCSA
DQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVE
TGEIKREYGGHQKAVVCLAFNDSVLG

Sequence of entity 3 (E), FASTA

>9TDT_3 Rapamycin-insensitive companion of mTOR (chains E)
MADYKDHDGDYKDHDIDYKDDDDKGTMAAIGRGRSLKNLRVRGRNDSGEENVPLDLTREP
SDNLREILQNVARLQGVSNMRKLGHLNNFTKLLCDIGHSEEKLGFHYEDIIICLRLALLN
EAKEVRAAGLRALRYLIQDSSILQKVLKLKVDYLIARCIDIQQSNEVERTQALRLVRKMI
TVNASLFPSSVTNSLIAVGNDGLQERDRMVRACIAIICELALQNPEVVALRGGLNTILKN
VIDCQLSRINEALITTILHLLNHPKTRQYVRADVELERILAPYTDFHYRHSPDTAEGQLK
EDREARFLASKMGIIATFRSWAGIINLCKPGNSGIQSLIGVLCIPNMEIRRGLLEVLYDI
FRLPLPVVTEEFIEALLSVDPGRFQDSWRLSDGFVAAEAKTILPHRARSRPDLMDNYLAL
ILSAFIRNGLLEGLVEVITNSDDHISVRATILLGELLHMANTILPHSHSHHLHCLPTLMN
MAASFDIPKEKRLRASAALNCLKRFHEMKKRGPKPYSLHLDHIIQKAIATHQKRDQYLRV
QKDIFILKDTEEALLINLRDSQVLQHKENLEWNWNLIGTILKWPNVNLRNYKDEQLHRFV
RRLLYFYKPSSKLYANLDLDFAKAKQLTVVGCQFTEFLLESEEDGQGYLEDLVKDIVQWL
NASSGMKPERSLQNNGLLTTLSQHYFLFIGTLSCHPHGVKMLEKCSVFQCLLNLCSLKNQ
DHLLKLTVSSLDYSRDGLARVILSKILTAATDACRLYATKHLRVLLRANVEFFNNWGIEL
LVTQLHDKNKTISSEALDILDEACEDKANLHALIQMKPALSHLGDKGLLLLLRFLSIPKG
FSYLNERGYVAKQLEKWHREYNSKYVDLIEEQLNEALTTYRKPVDGDNYVRRSNQRLQRP
HVYLPIHLYGQLVHHKTGCHLLEVQNIITELCRNVRTPDLDKWEEIKKLKASLWALGNIG
SSNWGLNLLQEENVIPDILKLAKQCEVLSIRGTCVYVLGLIAKTKQGCDILKCHNWDAVR
HSRKHLWPVVPDDVEQLCNELSSIPSTLSLNSESTSSRHNSESESVPSSMFILEDDRFGS
SSTSTFFLDINEDTEPTFYDRSGPIKDKNSFPFFASSKLVKNRILNSLTLPNKKHRSSSD
PKGGKLSSESKTSNRRIRTLTEPSVDFNHSDDFTPISTVQKTLQLETSFMGNKHIEDTGS
TPSIGENDLKFTKNFGTENHRENTSRERLVVESSTSSHMKIRSQSFNTDTTTSGISSMSS
SPSRETVGVDATTMDTDCGSMSTVVSTKTIKTSHYLTPQSNHLSLSKSNSVSLVPPGSSH
TLPRRAQSLKAPSIATIKSLADCNFSYTSSRDAFGYATLKRLQQQRMHPSLSHSEALASP
AKDVLFTDTITMKANSFESRLTPSRFMKALSYASLDKEDLLSPINQNTLQRSSSVRSMVS
SATYGGSDDYIGLALPVDINDIFQVKDIPYFQTKNIPPHDDRGARAFAHDAGGLPSGTGG
LVKNSFHLLRQQMSLTEIMNSIHSDASLFLESTEDTGLQEHTDDNCLYCVCIEILGFQPS
NQLSAICSHSDFQDIPYSDWCEQTIHNPLEVVPSKFSGISGCSDGVSQEGSASSTKSTEL
LLGVKTIPDDTPMCRILLRKEVLRLVINLSSSVSTKCHETGLLTIKEKYPQTFDDICLYS
EVSHLLSHCTFRLPCRRFIQELFQDVQFLQMHEEAEAVLATPPKQPIVDTSAES

Sequence of entity 4 (G), FASTA

>9TDT_4 Target of rapamycin complex 2 subunit MAPKAP1 (chains G)
XAFLDNPTIILAHIRQSHVTSDDTGMCEMVLIDHDVDLEKIHPPSMPGDSGSEIQGSNGE
TQGYVYAQSVDITSSWDFGIRRRSNTAQRLERLRKERQNQIKCKNIQWKERNSKQSAQEL
KSLFEKKSLKEKPPISGKQSILSVRLEQCPLQLNNPFNEYSKFDGKGHVGTTATKKIDVY
LPLHSSQDRLLPMTVVTMASARVQDLIGLICWQYTSEGREPKLNDNVSAYCLHIAEDDGE
VDTDFPPLDSNEPIHKFGFSTLALVEKYSSPGLTSKESLFVRINAAHGFSLIQVDNTKVT
MKEILLKAVKRRKGSQKVSGPQYRLEKQSEPNVAVDLDSTLESQSAWEFCLVRENSSRAD
GVFEEDSQIDIATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKAS
TKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVL
KVNYILESRASTARADYFAQKQRKLNRRTSFSFQKEKKSGQQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Primary citation

Structural basis for a phosphoinositide-driven mTORC2-AKT positive feedback loop. Hay, I.M., Bourguet, M., Ahsan, B. et al. bioRxiv (2026). DOI 10.64898/2026.01.08.698367

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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