9F42: LST2 TOS peptide

cryo-EM structure of LST2 TOS peptide bound to human mTOR complex 1, focused on RAPTOR. Determined by electron microscopy at 3.27 Å resolution. Released 14 Aug 2024.

Method: Electron microscopy
Resolution: 3.27 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,465
Mol. weight: 154.43 kDa
Released: 14 Aug 2024

Explore 9F42 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F42 contains 48 α-helices and 39 β-strands across 1 chain. 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 E: 48 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	20-24	5
α-helix	33-36	4
α-helix	41-45	5
β-strand	57-64	8	1
β-strand	85	1	2
β-strand	88	1	2
α-helix	90-92	3
α-helix	95-111	17
β-strand	118-123	6	1
α-helix	127-140	14
β-strand	145-151	7	1
α-helix	156-158	3
β-strand	159	1	3
β-strand	163-167	5	3
β-strand	174-178	5	3
α-helix	179-185	7
β-strand	191-195	5	1
α-helix	199-218	20
β-strand	241-244	4	1
α-helix	263-268	6
α-helix	270-278	9
α-helix	282-286	5
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	1
α-helix	370-372	3
α-helix	378-391	14
α-helix	393-398	6
α-helix	404-406	3
α-helix	408-421	14
α-helix	429-430	2
α-helix	433-441	9
α-helix	446-457	12
α-helix	461-470	10
α-helix	473-478	6
α-helix	479-481	3
α-helix	487-501	15
α-helix	505-511	7
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	589-597	9
α-helix	600-604	5
α-helix	605-609	5
α-helix	613-627	15
α-helix	635-648	14
α-helix	657-673	17
α-helix	675-684	10
α-helix	807-819	13
α-helix	824-838	15
α-helix	951-953	3
α-helix	959-964	6
α-helix	965-967	3
α-helix	974-975	2
α-helix	983-1007	25
β-strand	1015-1016	2	4
β-strand	1028-1031	4	5
β-strand	1038-1041	4	5
β-strand	1046-1049	4	5
β-strand	1056-1060	5	5
β-strand	1070-1076	7	6
β-strand	1083-1088	6	6
β-strand	1092-1097	6	6
β-strand	1107-1113	7	6
β-strand	1127-1131	5	7
β-strand	1137-1142	6	7
β-strand	1146-1151	6	7
β-strand	1156-1162	7	7
β-strand	1169-1173	5	8
β-strand	1181-1185	5	8
β-strand	1190-1193	4	8
β-strand	1203-1207	5	8
β-strand	1214-1218	5	9
β-strand	1227-1231	5	9
β-strand	1235-1240	6	9
β-strand	1243-1251	9	9
β-strand	1259-1260	2	10
β-strand	1267-1270	4	10
β-strand	1276-1281	6	10
β-strand	1288-1291	4	10
β-strand	1306-1309	4	4
β-strand	1316-1319	4	4
β-strand	1325-1329	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulatory-associated protein of mTOR	E	protein	1363	Homo sapiens	Q8N122 (AlphaFold model)
Lateral signaling target protein 2 homolog	G	protein	13	Homo sapiens	Q9HCC9 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>9F42_1 Regulatory-associated protein of mTOR (chains E)
HHHHHHHHHHEQKLISEEDLDYKDDDDKMESEMLQSPLLGLGEEDEADLTDWNLPLAFMK
KRHCEKIEGSKSLAQSWRMKDRMKTVSVALVLCLNVGVDPPDVVKTTPCARLECWIDPLS
MGPQKALETIGANLQKQYENWQPRARYKQSLDPTVDEVKKLCTSLRRNAKEERVLFHYNG
HGVPRPTVNGEVWVFNKNYTQYIPLSIYDLQTWMGSPSIFVYDCSNAGLIVKSFKQFALQ
REQELEVAAINPNHPLAQMPLPPSMKNCIQLAACEATELLPMIPDLPADLFTSCLTTPIK
IALRWFCMQKCVSLVPGVTLDLIEKIPGRLNDRRTPLGELNWIFTAITDTIAWNVLPRDL
FQKLFRQDLLVASLFRNFLLAERIMRSYNCTPVSSPRLPPTYMHAMWQAWDLAVDICLSQ
LPTIIEEGTAFRHSPFFAEQLTAFQVWLTMGVENRNPPEQLPIVLQVLLSQVHRLRALDL
LGRFLDLGPWAVSLALSVGIFPYVLKLLQSSARELRPLLVFIWAKILAVDSSCQADLVKD
NGHKYFLSVLADPYMPAEHRTMTAFILAVIVNSYHTGQEACLQGNLIAICLEQLNDPHPL
LRQWVAICLGRIWQNFDSARWCGVRDSAHEKLYSLLSDPIPEVRCAAVFALGTFVGNSAE
RTDHSTTIDHNVAMMLAQLVSDGSPMVRKELVVALSHLVVQYESNFCTVALQFIEEEKNY
ALPSPATTEGGSLTPVRDSPCTPRLRSVSSYGNIRAVATARSLNKSLQNLSLTEESGGAV
AFSPGNLSTSSSASSTLGSPENEEHILSFETIDKMRRASSYSSLNSLIGVSFNSVYTQIW
RVLLHLAADPYPEVSDVAMKVLNSIAYKATVNARPQRVLDTSSLTQSAPASPTNKGVHIH
QAGGSPPASSTSSSSLTNDVAKQPVSRDLPSGRPGTTGPAGAQYTPHSHQFPRTRKMFDK
GPEQTADDADDAAGHKSFISATVQTGFCDWSARYFAQPVMKIPEEHDLESQIRKEREWRF
LRNSRVRRQAQQVIQKGITRLDDQIFLNRNPGVPSVVKFHPFTPCIAVADKDSICFWDWE
KGEKLDYFHNGNPRYTRVTAMEYLNGQDCSLLLTATDDGAIRVWKNFADLEKNPEMVTAW
QGLSDMLPTTRGAGMVVDWEQETGLLMSSGDVRIVRIWDTDREMKVQDIPTGADSCVTSL
SCDSHRSLIVAGLGDGSIRVYDRRMALSECRVMTYREHTAWVVKASLQKRPDGHIVSVSV
NGDVRIFDPRMPESVNVLQIVKGLTALDIHPQADLIACGSVNQFTAIYNSSGELINNIKY
YDGFMGQRVGAISCLAFHPHWPHLAVGSNDYYISVYSVEKRVR

Sequence of entity 2 (G), FASTA

>9F42_2 Lateral signaling target protein 2 homolog (chains G)
DEEERVFFMDDVE

Primary citation

mTORC1 phosphorylates and stabilizes LST2 to negatively regulate EGFR. Battaglioni, S., Craigie, L.M., Filippini, S. et al. Proc Natl Acad Sci U S A (2024) 121:e2405959121-e2405959121. DOI 10.1073/pnas.2405959121 · PubMed

Other PDB entries of the same protein (UniProt Q8N122 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ERA 2.86 Å, RMC-5552 in complex with mTORC1 and FKBP12
7UX2 2.9 Å, cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex
8RCN 3.1 Å, CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458…
6U62 3.18 Å, Raptor-Rag-Ragulator complex
7UXC 3.2 Å, cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with symmetry expansion
7UXH 3.2 Å, cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex
6BCX 3.23 Å, mTORC1 structure refined to 3.0 angstroms
9ED4 3.23 Å, A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane
8RCK 3.4 Å, CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458…
9F43 3.49 Å, cryo-EM structure of human LST2 bound to human mTOR complex 1, focused on RAPTOR
7PEB 3.67 Å, cryo-EM structure of DEPTOR bound to human mTOR complex 1, focussed on one protomer
9F44 3.68 Å, cryo-EM structure of LST2 TOS peptide bound to human mTOR complex 1

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