8RCK: Serine/threonine-protein kinase mTOR

CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused on one protomer copy. Determined by electron microscopy at 3.4 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 27,252
Mol. weight: 487.52 kDa
Ligands: MG, ANP
Released: 11 Sept 2024

Explore 8RCK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RCK contains 191 α-helices and 87 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 B: 136 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	62-73	12
α-helix	83-91	9
α-helix	107-114	8
α-helix	122-134	13
α-helix	139-154	16
α-helix	167-178	12
α-helix	180-183	4
α-helix	187-197	11
α-helix	204-211	8
α-helix	214-217	4
α-helix	218-222	5
α-helix	234-243	10
α-helix	262-273	12
α-helix	278-286	9
α-helix	387-402	16
α-helix	411-422	12
α-helix	436-443	8
α-helix	448-454	7
α-helix	456-459	4
α-helix	460-462	3
α-helix	484-487	4
α-helix	488-490	3
α-helix	498-509	12
α-helix	515-527	13
α-helix	529-531	3
α-helix	532-548	17
α-helix	579-591	13
α-helix	601-611	11
α-helix	616-630	15
α-helix	646-665	20
α-helix	669-677	9
α-helix	681-683	3
α-helix	690-700	11
α-helix	705-718	14
α-helix	723-725	3
α-helix	727-743	17
α-helix	749-759	11
α-helix	765-784	20
α-helix	792-809	18
α-helix	810-816	7
α-helix	817-829	13
α-helix	839-851	13
α-helix	857-860	4
α-helix	863-872	10
α-helix	878-888	11
α-helix	892-895	4
α-helix	896-902	7
α-helix	934-938	5
α-helix	943-959	17
α-helix	962-966	5
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	1031-1040	10
α-helix	1046-1062	17
α-helix	1067-1069	3
α-helix	1071-1073	3
α-helix	1075-1083	9
α-helix	1091-1100	10
α-helix	1104-1107	4
α-helix	1111-1114	4
α-helix	1117-1122	6
α-helix	1129-1142	14
α-helix	1149-1151	3
α-helix	1152-1165	14
α-helix	1167-1169	3
α-helix	1170-1184	15
α-helix	1185-1191	7
α-helix	1192-1199	8
α-helix	1207-1218	12
α-helix	1263-1268	6
α-helix	1277-1293	17
α-helix	1298-1301	4
α-helix	1304-1310	7
α-helix	1312-1328	17
α-helix	1331-1347	17
α-helix	1351-1365	15
α-helix	1377-1379	3
α-helix	1380-1389	10
α-helix	1393-1404	12
α-helix	1410-1422	13
α-helix	1426-1439	14
α-helix	1514-1520	7
α-helix	1529-1532	4
α-helix	1541-1545	5
α-helix	1557-1571	15
α-helix	1573-1577	5
α-helix	1587-1607	21
α-helix	1609-1624	16
α-helix	1630-1640	11
α-helix	1650-1658	9
α-helix	1668-1677	10
α-helix	1687-1690	4
α-helix	1694-1705	12
α-helix	1710-1727	18
α-helix	1728-1730	3
α-helix	1737-1762	26
α-helix	1769-1782	14
α-helix	1787-1812	26
α-helix	1868-1893	26
α-helix	1900-1913	14
α-helix	1917-1928	12
α-helix	1932-1938	7
α-helix	1951-1967	17
α-helix	1969-1971	3
α-helix	1973-1979	7
α-helix	1985-2001	17
α-helix	2005-2020	16
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	2149-2151	3
β-strand	2152	1	2
β-strand	2153-2156	4	1
β-strand	2159-2162	4	1
α-helix	2163-2164	2
β-strand	2170-2176	7	1
β-strand	2181-2188	8	1
α-helix	2193-2210	18
α-helix	2213-2217	5
β-strand	2227-2231	5	1
β-strand	2234-2238	5	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
β-strand	2344-2347	4	3
β-strand	2353-2355	3	3
α-helix	2363-2366	4
α-helix	2381-2384	4
α-helix	2395-2409	15
α-helix	2411-2422	12
α-helix	2429-2432	4
α-helix	2493-2509	17
α-helix	2521-2533	13
α-helix	2535-2538	4

Chain E: 1 helix, 30 β-strands

Element	Residues	Length	Sheet
β-strand	14-19	6	4
β-strand	23-28	6	4
β-strand	34-39	6	4
β-strand	47-50	4	5
β-strand	56-60	5	5
β-strand	62-69	8	5
β-strand	81-87	7	5
β-strand	91-93	3	6
β-strand	99-102	4	6
β-strand	104	1	7
β-strand	105	1	5
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	173-176	4	8
β-strand	187-189	3	8
β-strand	193-199	7	8
β-strand	210-217	8	8
β-strand	225-228	4	9
β-strand	234-238	5	9
β-strand	243-248	6	9
β-strand	253-259	7	9
α-helix	265-267	3
β-strand	276-279	4	10
β-strand	284-287	4	10
β-strand	294-298	5	10
β-strand	306-308	3	10
β-strand	315-320	6	4

Chain Y: 54 helices, 45 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
α-helix	31-34	4
α-helix	43-46	4
β-strand	57-64	8	11
α-helix	79-81	3
β-strand	85	1	12
β-strand	88	1	12
α-helix	90-92	3
α-helix	97-111	15
α-helix	117	1
β-strand	118-123	6	11
α-helix	128-140	13
β-strand	145-150	6	11
α-helix	156-158	3
β-strand	164	1	13
β-strand	175	1	13
α-helix	179-185	7
β-strand	190-194	5	11
α-helix	199-217	19
β-strand	240-244	5	11
α-helix	262-268	7
α-helix	273-281	9
α-helix	292-295	4
α-helix	308-327	20
α-helix	330-337	8
α-helix	341-358	18
β-strand	365-367	3	11
α-helix	378-398	21
α-helix	401-406	6
α-helix	408-419	12
α-helix	420-422	3
α-helix	428-430	3
α-helix	433-439	7
α-helix	446-457	12
α-helix	461-470	10
α-helix	473-479	7
α-helix	488-501	14
α-helix	508-511	4
α-helix	514-523	10
α-helix	529-546	18
α-helix	549-555	7
α-helix	558-565	8
α-helix	571-584	14
α-helix	590-597	8
α-helix	601-604	4
α-helix	605-609	5
α-helix	613-630	18
α-helix	635-637	3
α-helix	638-650	13
α-helix	651-653	3
α-helix	657-678	22
α-helix	682-685	4
α-helix	807-820	14
α-helix	824-839	16
α-helix	959-964	6
α-helix	965-968	4
α-helix	974-975	2
α-helix	976-978	3
α-helix	983-1007	25
β-strand	1015-1021	7	14
β-strand	1028-1031	4	15
β-strand	1037-1041	5	15
β-strand	1045-1050	6	15
α-helix	1055	1
β-strand	1056-1061	6	15
α-helix	1064-1065	2
β-strand	1070-1075	6	16
β-strand	1084-1088	5	16
β-strand	1092-1096	5	16
β-strand	1108-1113	6	16
β-strand	1127-1132	6	17
β-strand	1137-1142	6	17
β-strand	1147-1151	5	17
β-strand	1156-1161	6	17
β-strand	1169	1	18
β-strand	1173-1175	3	19
β-strand	1180-1182	3	19
β-strand	1185	1	18
β-strand	1190	1	20
β-strand	1192-1194	3	19
β-strand	1207	1	20
α-helix	1213	1
β-strand	1214	1	21
β-strand	1218-1219	2	22
β-strand	1227-1230	4	22
β-strand	1231	1	21
β-strand	1236-1239	4	22
β-strand	1246-1249	4	22
β-strand	1261-1262	2	23
β-strand	1267-1268	2	23
β-strand	1277	1	24
β-strand	1280-1281	2	23
α-helix	1285	1
β-strand	1286	1	23
α-helix	1287-1288	2
β-strand	1290	1	24
β-strand	1304-1309	6	14
β-strand	1316-1320	5	14
β-strand	1324-1329	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase mTOR	B	protein	2549	Homo sapiens	P42345 (AlphaFold model)
Target of rapamycin complex subunit LST8	E	protein	326	Homo sapiens	Q9BVC4 (AlphaFold model)
Regulatory-associated protein of mTOR	Y	protein	1335	Homo sapiens	Q8N122 (AlphaFold model)
Eukaryotic translation initiation factor 4E-binding protein 1	X	protein	118	Homo sapiens	Q13541 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8RCK_1 Serine/threonine-protein kinase mTOR (chains B)
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 (E), FASTA

>8RCK_2 Target of rapamycin complex subunit LST8 (chains E)
MNTSPGTVGSDPVILATAGYDHTVRFWQAHSGICTRTVQHQDSQVNALEVTPDRSMIAAA
GYQHIRMYDLNSNNPNPIISYDGVNKNIASVGFHEDGRWMYTGGEDCTARIWDLRSRNLQ
CQRIFQVNAPINCVCLHPNQAELIVGDQSGAIHIWDLKTDHNEQLIPEPEVSITSAHIDP
DASYMAAVNSTGNCYVWNLTGGIGDEVTQLIPKTKIPAHTRYALQCRFSPDSTLLATCSA
DQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVE
TGEIKREYGGHQKAVVCLAFNDSVLG

Sequence of entity 3 (Y), FASTA

>8RCK_3 Regulatory-associated protein of mTOR (chains Y)
MESEMLQSPLLGLGEEDEADLTDWNLPLAFMKKRHCEKIEGSKSLAQSWRMKDRMKTVSV
ALVLCLNVGVDPPDVVKTTPCARLECWIDPLSMGPQKALETIGANLQKQYENWQPRARYK
QSLDPTVDEVKKLCTSLRRNAKEERVLFHYNGHGVPRPTVNGEVWVFNKNYTQYIPLSIY
DLQTWMGSPSIFVYDCSNAGLIVKSFKQFALQREQELEVAAINPNHPLAQMPLPPSMKNC
IQLAACEATELLPMIPDLPADLFTSCLTTPIKIALRWFCMQKCVSLVPGVTLDLIEKIPG
RLNDRRTPLGELNWIFTAITDTIAWNVLPRDLFQKLFRQDLLVASLFRNFLLAERIMRSY
NCTPVSSPRLPPTYMHAMWQAWDLAVDICLSQLPTIIEEGTAFRHSPFFAEQLTAFQVWL
TMGVENRNPPEQLPIVLQVLLSQVHRLRALDLLGRFLDLGPWAVSLALSVGIFPYVLKLL
QSSARELRPLLVFIWAKILAVDSSCQADLVKDNGHKYFLSVLADPYMPAEHRTMTAFILA
VIVNSYHTGQEACLQGNLIAICLEQLNDPHPLLRQWVAICLGRIWQNFDSARWCGVRDSA
HEKLYSLLSDPIPEVRCAAVFALGTFVGNSAERTDHSTTIDHNVAMMLAQLVSDGSPMVR
KELVVALSHLVVQYESNFCTVALQFIEEEKNYALPSPATTEGGSLTPVRDSPCTPRLRSV
SSYGNIRAVATARSLNKSLQNLSLTEESGGAVAFSPGNLSTSSSASSTLGSPENEEHILS
FETIDKMRRASSYSSLNSLIGVSFNSVYTQIWRVLLHLAADPYPEVSDVAMKVLNSIAYK
ATVNARPQRVLDTSSLTQSAPASPTNKGVHIHQAGGSPPASSTSSSSLTNDVAKQPVSRD
LPSGRPGTTGPAGAQYTPHSHQFPRTRKMFDKGPEQTADDADDAAGHKSFISATVQTGFC
DWSARYFAQPVMKIPEEHDLESQIRKEREWRFLRNSRVRRQAQQVIQKGITRLDDQIFLN
RNPGVPSVVKFHPFTPCIAVADKDSICFWDWEKGEKLDYFHNGNPRYTRVTAMEYLNGQD
CSLLLTATDDGAIRVWKNFADLEKNPEMVTAWQGLSDMLPTTRGAGMVVDWEQETGLLMS
SGDVRIVRIWDTDREMKVQDIPTGADSCVTSLSCDSHRSLIVAGLGDGSIRVYDRRMALS
ECRVMTYREHTAWVVKASLQKRPDGHIVSVSVNGDVRIFDPRMPESVNVLQIVKGLTALD
IHPQADLIACGSVNQFTAIYNSSGELINNIKYYDGFMGQRVGAISCLAFHPHWPHLAVGS
NDYYISVYSVEKRVR

Sequence of entity 4 (X), FASTA

>8RCK_4 Eukaryotic translation initiation factor 4E-binding protein 1 (chains X)
MSGGSSCSQTPSRAIPATRRVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRKFLM
ECRNSPVTKTPPRDLPTIPGVTSPSSDEPPMEASQSHLRNSPEDKRAGGEESQFEMDI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Primary citation

CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused on one protomer copy. Anandapadamanaban, M., Hay, I.M., Perisic, O. et al. To be published.

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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