7PEA: DEPTOR

cryo-EM structure of DEPTOR bound to human mTOR complex 1, overall refinement. Determined by electron microscopy at 4.07 Å resolution. Released 8 Sept 2021.

Method: Electron microscopy
Resolution: 4.07 Å
Organism: Homo sapiens
Chains: 8
Atoms: 58,252
Mol. weight: 1052.77 kDa
Ligands: IHP
Released: 8 Sept 2021

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

Secondary structure: helices and β-sheets

7PEA contains 404 α-helices and 210 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.

Chains A and B: 149 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	19-29	11
α-helix	38-52	15
α-helix	61-73	13
α-helix	83-97	15
α-helix	101-114	14
α-helix	122-134	13
α-helix	141-155	15
α-helix	165-178	14
α-helix	180-183	4
α-helix	184-186	3
α-helix	188-197	10
α-helix	204-222	19
α-helix	234-245	12
α-helix	262-275	14
α-helix	277-288	12
α-helix	308-311	4
α-helix	314-316	3
α-helix	357-360	4
α-helix	362-370	9
α-helix	372-375	4
α-helix	387-402	16
α-helix	411-425	15
α-helix	430-443	14
α-helix	447-451	5
α-helix	452-462	11
α-helix	479-490	12
α-helix	501-511	11
α-helix	515-527	13
α-helix	532-548	17
α-helix	579-591	13
α-helix	601-611	11
α-helix	616-629	14
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	705-717	13
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	792-809	18
α-helix	814-828	15
α-helix	837-851	15
α-helix	856-860	5
α-helix	864-874	11
α-helix	878-890	13
α-helix	896-902	7
α-helix	934-940	7
α-helix	943-959	17
α-helix	963-966	4
α-helix	968-982	15
α-helix	984-989	6
α-helix	990-1003	14
α-helix	1007-1023	17
α-helix	1024-1027	4
α-helix	1028-1041	14
α-helix	1046-1063	18
α-helix	1064-1069	6
α-helix	1071-1083	13
α-helix	1088-1090	3
α-helix	1091-1103	13
α-helix	1104-1110	7
α-helix	1111-1123	13
α-helix	1129-1145	17
α-helix	1152-1165	14
α-helix	1170-1184	15
α-helix	1185-1191	7
α-helix	1192-1201	10
α-helix	1207-1218	12
α-helix	1264-1269	6
α-helix	1277-1294	18
α-helix	1298-1301	4
α-helix	1304-1309	6
α-helix	1311-1316	6
α-helix	1318-1328	11
α-helix	1332-1346	15
α-helix	1351-1366	16
α-helix	1377-1379	3
α-helix	1382-1389	8
α-helix	1393-1406	14
α-helix	1410-1422	13
α-helix	1426-1440	15
α-helix	1447-1453	7
α-helix	1456-1469	14
α-helix	1471-1472	2
α-helix	1474-1487	14
α-helix	1490-1499	10
α-helix	1506-1523	18
α-helix	1526-1535	10
α-helix	1541-1553	13
α-helix	1557-1580	24
α-helix	1582-1607	26
α-helix	1609-1611	3
α-helix	1612-1625	14
α-helix	1630-1640	11
α-helix	1646-1648	3
α-helix	1650-1662	13
α-helix	1666-1677	12
α-helix	1688-1690	3
α-helix	1694-1706	13
α-helix	1710-1731	22
α-helix	1738-1761	24
α-helix	1768-1782	15
α-helix	1787-1808	22
α-helix	1809-1813	5
α-helix	1868-1895	28
α-helix	1900-1913	14
α-helix	1917-1929	13
α-helix	1934-1938	5
α-helix	1939-1944	6
α-helix	1951-1966	16
α-helix	1969-1971	3
α-helix	1973-1980	8
α-helix	1985-2001	17
α-helix	2004-2020	17
α-helix	2023-2035	13
α-helix	2036-2041	6
α-helix	2044-2058	15
α-helix	2065-2070	6
α-helix	2071-2075	5
α-helix	2076-2090	15
α-helix	2094-2114	21
α-helix	2115-2117	3
β-strand	2120-2122	3	34
α-helix	2123-2126	4
α-helix	2128-2132	5
β-strand	2134	1	35
β-strand	2139	1	36
α-helix	2140	1
α-helix	2149-2150	2
β-strand	2152	1	36
β-strand	2153-2156	4	35
β-strand	2159-2161	3	34
β-strand	2170	1	37
β-strand	2173-2176	4	35
β-strand	2181-2183	3	35
β-strand	2184-2187	4	37
α-helix	2193-2211	19
α-helix	2213-2218	6
β-strand	2227-2229	3	37
β-strand	2235-2238	4	37
α-helix	2239-2240	2
β-strand	2243-2245	3	38
α-helix	2246-2256	11
α-helix	2263-2271	9
α-helix	2275-2277	3
α-helix	2280-2292	13
α-helix	2298-2306	9
α-helix	2310-2334	25
α-helix	2341-2343	3
β-strand	2344-2347	4	38
β-strand	2353-2355	3	38
α-helix	2364-2367	4
α-helix	2381-2386	6
α-helix	2395-2409	15
α-helix	2411-2423	13
α-helix	2428-2434	7
α-helix	2493-2509	17
α-helix	2521-2533	13
α-helix	2535-2540	6
α-helix	2543-2545	3

Chains C and D: 2 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	39
β-strand	15-19	5	40
β-strand	23	1	41
β-strand	24-27	4	40
β-strand	36	1	40
β-strand	39	1	41
β-strand	47-50	4	42
β-strand	56	1	43
β-strand	57-60	4	42
β-strand	65-67	3	42
β-strand	69	1	43
α-helix	75-77	3
β-strand	79-81	3	42
β-strand	88-91	4	44
β-strand	99-104	6	44
β-strand	108-113	6	44
β-strand	124-126	3	44
β-strand	134-136	3	45
β-strand	142-145	4	45
β-strand	152	1	46
β-strand	153-156	4	45
β-strand	165	1	46
β-strand	173-178	6	47
β-strand	184-189	6	47
β-strand	193-199	7	47
α-helix	200	1
β-strand	210-217	8	47
β-strand	223-228	6	48
β-strand	234-239	6	48
β-strand	243-248	6	48
β-strand	254-259	6	48
β-strand	273	1	49
β-strand	277-278	2	50
β-strand	284-288	5	50
β-strand	289	1	49
β-strand	294-298	5	50
β-strand	304-308	5	50
β-strand	315-318	4	40
β-strand	321	1	39

Chains E and F: 49 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
α-helix	33-36	4
α-helix	41-45	5
β-strand	59-64	6	51
β-strand	85	1	52
β-strand	88	1	52
α-helix	90-93	4
α-helix	95-113	19
β-strand	118-123	6	51
α-helix	127-140	14
β-strand	146-151	6	51
α-helix	156-158	3
β-strand	159	1	53
β-strand	163-167	5	53
β-strand	174-178	5	53
α-helix	179-185	7
β-strand	190-195	6	51
α-helix	199-218	20
β-strand	240-244	5	51
α-helix	262-268	7
α-helix	270-278	9
α-helix	282-284	3
α-helix	292-296	5
α-helix	308-327	20
α-helix	330-337	8
α-helix	341-358	18
β-strand	365-366	2	51
α-helix	369-372	4
α-helix	378-389	12
α-helix	393-394	2
α-helix	395-399	5
α-helix	404-406	3
α-helix	408-421	14
α-helix	429-430	2
α-helix	433-439	7
α-helix	446-458	13
α-helix	461-470	10
α-helix	473-478	6
α-helix	479-481	3
α-helix	487-501	15
α-helix	503-505	3
α-helix	506-511	6
α-helix	514-522	9
α-helix	529-542	14
α-helix	547-555	9
α-helix	558-564	7
α-helix	571-584	14
α-helix	589-598	10
α-helix	600-604	5
α-helix	605-609	5
α-helix	613-628	16
α-helix	635-648	14
α-helix	657-673	17
α-helix	675-684	10
α-helix	808-819	12
α-helix	824-838	15
α-helix	951-953	3
α-helix	959-968	10
α-helix	974-975	2
α-helix	983-1007	25
β-strand	1015-1021	7	54
β-strand	1028-1031	4	55
β-strand	1038-1041	4	55
β-strand	1046-1049	4	55
β-strand	1056-1059	4	55
β-strand	1070-1076	7	56
β-strand	1083-1088	6	56
β-strand	1092-1097	6	56
β-strand	1107-1113	7	56
β-strand	1127-1128	2	57
β-strand	1131-1132	2	58
β-strand	1137-1138	2	58
β-strand	1141-1142	2	57
β-strand	1146-1151	6	58
β-strand	1156-1162	7	58
β-strand	1169-1173	5	59
β-strand	1181-1185	5	59
β-strand	1190-1193	4	59
β-strand	1203-1207	5	59
β-strand	1214	1	60
β-strand	1218	1	61
β-strand	1227-1230	4	61
β-strand	1231	1	60
β-strand	1235-1239	5	61
β-strand	1248-1251	4	61
β-strand	1260-1261	2	62
β-strand	1267-1269	3	62
β-strand	1278-1281	4	62
β-strand	1288-1289	2	62
β-strand	1306-1309	4	54
β-strand	1316-1319	4	54
β-strand	1324-1329	6	54

Chains I and J: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	326	1	63
β-strand	329-333	5	64
β-strand	342-344	3	65
β-strand	351	1	66
β-strand	352-355	4	65
α-helix	360-363	4
β-strand	371	1	66
β-strand	372-375	4	64
β-strand	378-379	2	64
α-helix	385-394	10
β-strand	399-403	5	64
β-strand	406	1	63

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase mTOR	A, B	protein	2549	Homo sapiens	P42345 (AlphaFold model)
Target of rapamycin complex subunit LST8	C, D	protein	326	Homo sapiens	Q9BVC4 (AlphaFold model)
Regulatory-associated protein of mTOR	E, F	protein	1396	Homo sapiens	Q8N122 (AlphaFold model)
DEP domain-containing mTOR-interacting protein	I, J	protein	409	Homo sapiens	Q8TB45 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7PEA_1 Serine/threonine-protein kinase mTOR (chains A, B)
MLGTGPAAATTAATTSXXXXXXXXXXXXXXSRNEETXXXXXXXXXXXXXXXXXEMSQEES
TRFYDQLNHHIFELVSSSDANERKGGILAIASLIGVEGGNATRIGRFANYLRNLLPSNDP
VVMEMASKAIGRLAMAGDTFTAEYVEFEVKRALEWLGADRNEGRRHAAVLVLRELAISVP
TFFFQQVQPFFDNIFVAVWDPKQAIREGAVAALRACLILTTQREPKEMQKPQWYRHTFEE
AEKGFDETLAKEKGMNRDDRIHGALLILNELVRISSMEGERLREEMEEITQQQLVHDKYC
KDLMGFGTKPRHITPFTSFQAVQPQQSNALVGLLGYSSHQGLMGFGTSPSPAKSTXXXXX
XXXXXXXXXXXXXXXXXXXXRNSKNSLIQMTILNLLPRLAAFRPSAFTDTQYLQDTMNHV
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 (C, D), FASTA

>7PEA_2 Target of rapamycin complex subunit LST8 (chains C, D)
MNTSPGTVGSDPVILATAGYDHTVRFWQAHSGICTRTVQHQDSQVNALEVTPDRSMIAAA
GYQHIRMYDLNSNNPNPIISYDGVNKNIASVGFHEDGRWMYTGGEDCTARIWDLRSRNLQ
CQRIFQVNAPINCVCLHPNQAELIVGDQSGAIHIWDLKTDHNEQLIPEPEVSITSAHIDP
DASYMAAVNSTGNCYVWNLTGGIGDEVTQLIPKTKIPAHTRYALQCRFSPDSTLLATCSA
DQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVE
TGEIKREYGGHQKAVVCLAFNDSVLG

Sequence of entity 3 (E, F), FASTA

>7PEA_3 Regulatory-associated protein of mTOR (chains E, F)
MAHHHHHHHHHHGSTSGSGEQKLISEEDLGSTSGSGDYKDDDDKLTSLYKKAGLENLYFQ
GMESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLAQSWRMKDRMKTVS
VALVLCLNVGVDPPDVVKTTPCARLECWIDPLSMGPQKALETIGANLQKQYENWQPRARY
KQSLDPTVDEVKKLCTSLRRNAKEERVLFHYNGHGVPRPTVNGEVWVFNKNYTQYIPLSI
YDLQTWMGSPSIFVYDCSNAGLIVKSFKQFALQREQELEVAAINPNHPLAQMPLPPSMKN
CIQLAACEATELLPMIPDLPADLFTSCLTTPIKIALRWFCMQKCVSLVPGVTLDLIEKIP
GRLNDRRTPLGELNWIFTAITDTIAWNVLPRDLFQKLFRQDLLVASLFRNFLLAERIMRS
YNCTPVSSPRLPPTYMHAMWQAWDLAVDICLSQLPTIIEEGTAFRHSPFFAEQLTAFQVW
LTMGVENRNPPEQLPIVLQVLLSQVHRLRALDLLGRFLDLGPWAVSLALSVGIFPYVLKL
LQSSARELRPLLVFIWAKILAVDSSCQADLVKDNGHKYFLSVLADPYMPAEHRTMTAFIL
AVIVNSYHTGQEACLQGNLIAICLEQLNDPHPLLRQWVAICLGRIWQNFDSARWCGVRDS
AHEKLYSLLSDPIPEVRCAAVFALGTFVGNSAERTDHSTTIDHNVAMMLAQLVSDGSPMV
RKELVVALSHLVVQYESNFCTVALQFIEEEKNYALPSPATTEGGSLTPVRDSPCTPRLRS
VSSYGNIRAVATARSLNKSLQNLSLTEESGGAVAFSPGNLSTSSSASSTLGSPENEEHIL
SFETIDKMRRASSYSSLNSLIGVSFNSVYTQIWRVLLHLAADPYPEVSDVAMKVLNSIAY
KATVNARPQRVLDTSSLTQSAPASPTNKGVHIHQAGGSPPASSTSSSSLTNDVAKQPVSR
DLPSGRPGTTGPAGAQYTPHSHQFPRTRKMFDKGPEQTADDADDAAGHKSFISATVQTGF
CDWSARYFAQPVMKIPEEHDLESQIRKEREWRFLRNSRVRRQAQQVIQKGITRLDDQIFL
NRNPGVPSVVKFHPFTPCIAVADKDSICFWDWEKGEKLDYFHNGNPRYTRVTAMEYLNGQ
DCSLLLTATDDGAIRVWKNFADLEKNPEMVTAWQGLSDMLPTTRGAGMVVDWEQETGLLM
SSGDVRIVRIWDTDREMKVQDIPTGADSCVTSLSCDSHRSLIVAGLGDGSIRVYDRRMAL
SECRVMTYREHTAWVVKASLQKRPDGHIVSVSVNGDVRIFDPRMPESVNVLQIVKGLTAL
DIHPQADLIACGSVNQFTAIYNSSGELINNIKYYDGFMGQRVGAISCLAFHPHWPHLAVG
SNDYYISVYSVEKRVR

Sequence of entity 4 (I, J), FASTA

>7PEA_4 DEP domain-containing mTOR-interacting protein (chains I, J)
MEEGGSTGSAGSDSSTSGSGGAQQRELERMAEVLVTGEQLRLRLHEEKVIKDRRHHLKTY
PNCFVAKELIDWLIEHKEASDRETAIKLMQKLADRGIIHHVCDEHKEFKDVKLFYRFRKD
DGTFPLDNEVKAFMRGQRLYEKLMSPENTLLQPREEEGVKYERTFMASEFLDWLVQEGEA
TTRKEAEQLCHRLMEHGIIQHVSSKHPFVDSNLLYQFRMNFRRRRRLMELLNEKSPSSQE
THDSPFCLRKQSHDNRKSTSFMSVSPSKEIKIVSAVRRSSMSSCGSSGYFSSSPTLSSSP
PVLCNPKSVLKRPVTSEELLTPGAPYARKTFTIVGDAVGWGFVVRGSKPCHIQAVDPSGP
AAAAGMKVCQFVVSVNGLNVLHVDYRTVNNLILTGPRTIVMEVMEELEC

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	2

Primary citation

Regulation of human mTOR complexes by DEPTOR. Walchli, M., Berneiser, K., Mangia, F. et al. Elife (2021) 10. DOI 10.7554/eLife.70871 · 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

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