5WBY: MTOR(deltaN)-mLST8-PRAS40(beta-strand) complex

Crystal structure of mTOR(deltaN)-mLST8-PRAS40(beta-strand) complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 22,243
Mol. weight: 362.51 kDa
Released: 20 Dec 2017

Explore 5WBY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WBY contains 123 α-helices and 88 β-strands across 6 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: 59 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1386-1406	21
α-helix	1410-1421	12
α-helix	1426-1439	14
α-helix	1446-1452	7
α-helix	1456-1469	14
α-helix	1474-1487	14
α-helix	1490-1498	9
α-helix	1506-1523	18
α-helix	1526-1535	10
α-helix	1541-1553	13
α-helix	1557-1577	21
α-helix	1587-1602	16
α-helix	1613-1624	12
α-helix	1630-1640	11
α-helix	1650-1663	14
α-helix	1666-1677	12
α-helix	1688-1690	3
α-helix	1694-1706	13
α-helix	1710-1729	20
α-helix	1738-1761	24
α-helix	1768-1782	15
α-helix	1787-1813	27
α-helix	1868-1893	26
α-helix	1900-1913	14
α-helix	1917-1929	13
α-helix	1932-1938	7
α-helix	1939-1943	5
α-helix	1951-1966	16
α-helix	1973-1979	7
α-helix	1985-2020	36
α-helix	2023-2035	13
α-helix	2036-2040	5
α-helix	2044-2059	16
α-helix	2065-2073	9
α-helix	2075-2091	17
α-helix	2094-2114	21
β-strand	2120-2122	3	12
α-helix	2123-2126	4
α-helix	2128-2132	5
β-strand	2134	1	12
β-strand	2139	1	13
α-helix	2140	1
α-helix	2149-2150	2
β-strand	2152	1	13
β-strand	2153-2156	4	12
β-strand	2159-2162	4	12
β-strand	2170-2176	7	12
β-strand	2181-2187	7	12
α-helix	2193-2211	19
α-helix	2213-2217	5
β-strand	2227-2229	3	12
β-strand	2235-2238	4	12
α-helix	2239-2240	2
β-strand	2243-2245	3	14
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
β-strand	2344-2347	4	14
β-strand	2353-2355	3	14
α-helix	2364-2367	4
α-helix	2381-2386	6
α-helix	2395-2409	15
α-helix	2411-2422	12
α-helix	2429-2432	4
α-helix	2433-2435	3
α-helix	2493-2509	17
α-helix	2521-2533	13
α-helix	2535-2540	6
α-helix	2543-2545	3

Chain B: 61 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1386-1406	21
α-helix	1410-1421	12
α-helix	1426-1439	14
α-helix	1446-1452	7
α-helix	1456-1469	14
α-helix	1474-1487	14
α-helix	1490-1498	9
α-helix	1506-1523	18
α-helix	1526-1535	10
α-helix	1541-1553	13
α-helix	1557-1577	21
α-helix	1587-1605	19
α-helix	1613-1624	12
α-helix	1630-1640	11
α-helix	1650-1663	14
α-helix	1666-1677	12
α-helix	1688-1690	3
α-helix	1694-1706	13
α-helix	1710-1729	20
α-helix	1738-1761	24
α-helix	1768-1782	15
α-helix	1787-1813	27
α-helix	1868-1893	26
α-helix	1900-1913	14
α-helix	1917-1929	13
α-helix	1932-1938	7
α-helix	1939-1943	5
α-helix	1951-1966	16
α-helix	1969-1971	3
α-helix	1973-1980	8
α-helix	1985-2020	36
α-helix	2023-2035	13
α-helix	2036-2040	5
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
β-strand	2120-2122	3	1
α-helix	2123-2126	4
α-helix	2128-2132	5
β-strand	2134	1	1
β-strand	2139	1	2
α-helix	2140	1
α-helix	2149-2150	2
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	2193-2211	19
α-helix	2213-2217	5
β-strand	2227-2229	3	1
β-strand	2235-2238	4	1
α-helix	2239-2240	2
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	2298-2306	9
α-helix	2310-2334	25
β-strand	2344-2347	4	3
β-strand	2353-2355	3	3
α-helix	2364-2367	4
α-helix	2381-2386	6
α-helix	2395-2409	15
α-helix	2411-2422	12
α-helix	2429-2432	4
α-helix	2433-2435	3
α-helix	2493-2509	17
α-helix	2521-2533	13
α-helix	2535-2540	6
α-helix	2543-2545	3

Chain C: 1 helix, 30 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	15
β-strand	23-27	5	15
β-strand	34-39	6	15
β-strand	47-50	4	16
β-strand	56-60	5	16
β-strand	62	1	17
β-strand	65-69	5	16
β-strand	77-80	4	16
β-strand	87	1	17
β-strand	88-93	6	18
β-strand	99-104	6	18
β-strand	108-113	6	18
β-strand	123-126	4	18
α-helix	130	1
β-strand	131-136	6	19
β-strand	142-147	6	19
β-strand	152-156	5	19
β-strand	162-166	5	19
β-strand	173-178	6	20
β-strand	184-189	6	20
β-strand	194-199	6	20
β-strand	210-216	7	20
β-strand	223-228	6	21
β-strand	234-239	6	21
β-strand	243-248	6	21
β-strand	254-259	6	21
β-strand	273-278	6	22
β-strand	284-289	6	22
β-strand	293-298	6	22
β-strand	304-309	6	22
β-strand	315-322	8	15

Chain D: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	13-19	7	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	62	1	6
β-strand	65-69	5	5
β-strand	77-80	4	5
β-strand	87	1	6
β-strand	88-93	6	7
β-strand	99-104	6	7
β-strand	108-113	6	7
β-strand	123-126	4	7
α-helix	130	1
β-strand	131-136	6	8
β-strand	142-147	6	8
α-helix	151	1
β-strand	152-156	5	8
β-strand	162-166	5	8
β-strand	173-178	6	9
β-strand	184-189	6	9
β-strand	194-199	6	9
β-strand	210-216	7	9
β-strand	223-228	6	10
β-strand	234-239	6	10
β-strand	243-248	6	10
β-strand	254-259	6	10
β-strand	273-278	6	11
β-strand	284-289	6	11
β-strand	293-298	6	11
β-strand	304-309	6	11
β-strand	315-322	8	4

Chains O and P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	190-191	2	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase mTOR	A, B	protein	1177	Homo sapiens	P42345 (AlphaFold model)
Target of rapamycin complex subunit LST8	C, D	protein	328	Homo sapiens	Q9BVC4 (AlphaFold model)
Proline-rich AKT1 substrate 1	O, P	protein	98	Homo sapiens	Q96B36 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5WBY_1 Serine/threonine-protein kinase mTOR (chains A, B)
GTGDDNGIVLLGERAAKCRAYAKALHYKELEFQKGPTPAILESLISINNKLQQPEAAAGV
LEYAMKHFGELEIQATWYEKLHEWEDALVAYDKKMDTNKDDPELMLGRMRCLEALGEWGQ
LHQQCCEKWTLVNDETQAKMARMAAAAAWGLGQWDSMEEYTCMIPRDTHDGAFYRAVLAL
HQDLFSLAQQCIDKARDLLDAELTAMAGESYSRAYGAMVSCHMLSELEEVIQYKLVPERR
EIIRQIWWERLQGCQRIVEDWQKILMVRSLVVSPHEDMRTWLKYASLCGKSGRLALAHKT
LVLLLGVDPSRQLDHPLPTVHPQVTYAYMKNMWKSARKIDAFQHMQHFVQTMQQQAQHAI
ATEDQQHKQELHKLMARCFLKLGEWQLNLQGINESTIPKVLQYYSAATEHDRSWYKAWHA
WAVMNFEAVLHYKHQNQARDEKKKLRHASGANITNATTAATTAATATTTASTEGSNSESE
AESTENSPTPSPLQKKVTEDLSKTLLMYTVPAVQGFFRSISLSRGNNLQDTLRVLTLWFD
YGHWPDVNEALVEGVKAIQIDTWLQVIPQLIARIDTPRPLVGRLIHQLLTDIGRYHPQAL
IYPLTVASKSTTTARHNAANKILKNMCEHSNTLVQQAMMVSEELIRVAILWHEMWHEGLE
EASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQEWCRKYMKSG
NVKDLTQAWDLYYHVFRRISKQLPQLTSLELQYVSPKLLMCRDLELAVPGTYDPNQPIIR
IQSIAPSLQVITSKQRPRKLTLMGSNGHEFVFLLKGHEDLRQDERVMQLFGLVNTLLAND
PTSLRKNLSIQRYAVIPLSTNSGLIGWVPHCDTLHALIRDYREKKKILLNIEHRIMLRMA
PDYDHLTLMQKVEVFEHAVNNTAGDDLAKLLWLKSPSSEVWFDRRTNYTRSLAVMSMVGY
ILGLGDRHPSNLMLDRLSGKILHIDFGDCFEVAMTREKFPEKIPFRLTRMLTNAMEVTGL
DGNYRITCHTVMEVLREHKDSVMAVLEAFVYDPLLNWRLMDTNTKGNKRSRTRTDSYSAG
QSVEILDGVELGEPAHKKTGTTVPESIHSFIGDGLVKPEALNKKAIQIINRVRDKLTGRD
FSHDDTLDVPTQVELLIKQATSHENLCQCYIGWCPFW

Sequence of entity 2 (C, D), FASTA

>5WBY_2 Target of rapamycin complex subunit LST8 (chains C, D)
GSMNTSPGTVGSDPVILATAGYDHTVRFWQAHSGICTRTVQHQDSQVNALEVTPDRSMIA
AAGYQHIRMYDLNSNNPNPIISYDGVNKNIASVGFHEDGRWMYTGGEDCTARIWDLRSRN
LQCQRIFQVNAPINCVCLHPNQAELIVGDQSGAIHIWDLKTDHNEQLIPEPEVSITSAHI
DPDASYMAAVNSTGNCYVWNLTGGIGDEVTQLIPKTKIPAHTRYALQCRFSPDSTLLATC
SADQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWC
VETGEIKREYGGHQKAVVCLAFNDSVLG

Sequence of entity 3 (O, P), FASTA

>5WBY_3 Proline-rich AKT1 substrate 1 (chains O, P)
GSGRETSGEQLGISDNGGLFVMDEDATLQDLPPFCESDPESTDDGSLSEETPAGPPTCSV
PPASALPTQQYAKSLPVSVPVWGFKEKRTEARSSDEEN

Primary citation

Mechanisms of mTORC1 activation by RHEB and inhibition by PRAS40. Yang, H., Jiang, X., Li, B. et al. Nature (2017) 552:368-373. DOI 10.1038/nature25023 · 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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