7PE9: DEPTOR

cryo-EM structure of DEPTOR bound to human mTOR complex 2, DEPt-bound subset local refinement. Determined by electron microscopy at 3.7 Å resolution. Released 8 Sept 2021.

Method
Electron microscopy
Resolution
3.7 Å
Organism
Homo sapiens
Chains
5
Atoms
31,076
Mol. weight
626.05 kDa
Ligands
ACE, ZN, IHP
Released
8 Sept 2021

Explore 7PE9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PE9 contains 236 α-helices and 68 β-strands across 5 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: 141 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix18-2912
α-helix38-5215
α-helix61-7313
α-helix83-9311
α-helix102-11413
α-helix123-13412
α-helix141-15515
α-helix165-17814
α-helix182-1843
α-helix188-19710
α-helix204-22219
α-helix234-24512
α-helix262-27514
α-helix278-28811
α-helix308-3114
α-helix314-3163
α-helix357-3604
α-helix363-37513
α-helix387-40216
α-helix411-42414
α-helix430-44314
α-helix452-46211
α-helix480-49011
α-helix500-51112
α-helix515-52713
α-helix532-54615
α-helix581-59111
α-helix600-6067
α-helix609-6124
α-helix616-62813
α-helix649-66517
α-helix669-67810
α-helix681-6855
α-helix690-70011
α-helix705-71915
α-helix723-74321
α-helix747-76317
α-helix765-7684
α-helix769-7713
α-helix772-78312
α-helix792-80817
α-helix818-82811
α-helix838-8469
α-helix857-8604
α-helix864-87411
α-helix878-89114
α-helix896-9016
α-helix930-9367
α-helix943-95715
α-helix962-9643
α-helix968-98215
α-helix987-9893
α-helix990-100314
α-helix1007-102216
α-helix1028-104013
α-helix1050-106314
α-helix1067-10693
α-helix1071-10744
α-helix1075-10795
α-helix1088-10903
α-helix1091-110010
α-helix1111-11199
α-helix1129-114315
α-helix1153-116311
α-helix1170-118112
α-helix1186-11916
α-helix1192-120211
α-helix1207-121711
α-helix1229-12379
α-helix1265-12695
α-helix1277-129317
α-helix1298-13014
α-helix1304-13096
α-helix1312-13154
α-helix1318-132811
α-helix1331-134515
α-helix1351-136616
α-helix1371-13733
α-helix1377-13793
α-helix1380-13889
α-helix1393-140614
α-helix1410-142112
α-helix1426-143813
α-helix1447-14526
α-helix1457-146812
α-helix1476-148712
α-helix1490-150011
α-helix1506-152318
α-helix1526-15338
α-helix1541-155313
α-helix1557-157923
α-helix1585-15873
α-helix1590-160718
α-helix1609-16113
α-helix1615-16217
α-helix1630-163910
α-helix1646-16483
α-helix1650-166314
α-helix1666-167712
α-helix1688-16903
α-helix1694-170613
α-helix1710-172819
α-helix1739-176224
α-helix1768-178215
α-helix1787-180822
α-helix1878-189518
α-helix1900-191314
α-helix1917-192913
α-helix1939-19446
α-helix1951-196717
α-helix1973-19808
α-helix1985-200117
α-helix2003-202018
α-helix2023-203614
α-helix2037-20415
α-helix2045-205612
α-helix2065-20739
α-helix2075-209117
α-helix2094-211219
β-strand2120-212231
α-helix2123-21264
β-strand213912
α-helix21401
β-strand215212
β-strand2153-215643
β-strand2159-216241
α-helix21631
β-strand2170-217121
β-strand217314
β-strand2174-217633
β-strand218314
β-strand2184-218851
α-helix2193-221018
α-helix2213-22164
β-strand2227-222931
β-strand2234-223851
α-helix2239-22402
β-strand2243-224535
α-helix2246-225611
α-helix2263-22719
α-helix2275-22773
α-helix2280-229314
α-helix2298-23058
α-helix2310-233425
α-helix2341-23433
β-strand2344-234745
β-strand2353-235535
α-helix2364-23674
α-helix2381-23844
α-helix2395-240915
α-helix2411-242212
α-helix2429-24313
α-helix2495-250713
α-helix2521-253212
α-helix2535-25395
α-helix2543-25453
Chain C: 0 helices, 28 β-strands
ElementResiduesLengthSheet
β-strand14-1966
β-strand23-2756
β-strand34-3966
β-strand47-5047
β-strand56-6057
β-strand65-6957
β-strand79-8137
β-strand88-9368
β-strand99-10468
β-strand108-11368
β-strand124-12638
β-strand131-13669
β-strand142-14769
β-strand152-15659
β-strand162-16549
β-strand173-178610
β-strand185-189510
β-strand194-198510
β-strand211-216610
β-strand223-228611
β-strand234-239611
β-strand243-248611
β-strand254-259611
β-strand273-278612
β-strand284-289612
β-strand293-298612
β-strand306-308312
β-strand315-32176
Chain E: 75 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix33-4210
α-helix46-483
α-helix53-6917
α-helix81-899
α-helix97-11014
α-helix114-1229
α-helix126-1338
α-helix140-15617
α-helix158-1603
α-helix163-17412
α-helix185-19713
α-helix199-2046
α-helix207-21610
α-helix221-23414
α-helix241-2433
α-helix250-2545
α-helix255-2584
α-helix273-29220
α-helix295-3017
α-helix308-3147
α-helix315-3173
α-helix322-33413
α-helix346-3516
α-helix360-3623
α-helix370-3745
α-helix378-3792
β-strand386113
α-helix387-40216
α-helix404-41310
α-helix417-43418
α-helix441-4433
α-helix450-4578
α-helix463-48523
α-helix492-50413
α-helix525-53410
α-helix548-5558
α-helix568-58114
β-strand592114
α-helix598-61417
α-helix616-63722
α-helix647-6515
β-strand654114
α-helix655-6573
α-helix660-6645
α-helix670-67910
α-helix682-6876
α-helix696-7049
α-helix712-72211
α-helix726-7349
α-helix738-7414
α-helix747-7504
α-helix752-7576
α-helix758-7603
α-helix764-77714
α-helix781-7888
α-helix799-8057
α-helix806-8105
α-helix812-8187
α-helix824-8307
α-helix838-85013
β-strand877113
α-helix878-8803
α-helix882-8854
α-helix890-8989
α-helix902-9109
α-helix917-93317
α-helix937-9404
α-helix949-9557
α-helix962-97514
α-helix979-9879
β-strand990-992315
β-strand1428-1430315
α-helix1433-14353
α-helix1480-14845
α-helix1489-14935
α-helix1525-15284
α-helix1610-162213
α-helix1629-164214
α-helix1650-166213
α-helix1667-16726
α-helix1683-169311
Chain G: 5 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix7-2014
α-helix27-304
α-helix33-353
α-helix85-9915
β-strand104-10637
α-helix120-1234
Chain I: 15 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix21-233
α-helix24-285
α-helix29-4719
β-strand51-55516
β-strand58-63616
β-strand64-65217
α-helix66-7611
α-helix82-9514
β-strand98-100317
β-strand114-117417
α-helix118-1203
α-helix128-14417
β-strand152-156518
β-strand159-164618
β-strand165-166219
α-helix167-17711
α-helix183-19614
β-strand199-201319
α-helix206-2083
β-strand214-217419
α-helix224-2263
α-helix227-2293
α-helix316-3205
β-strand329-333520
β-strand342-344321
β-strand351122
β-strand352-355421
α-helix360-3634
β-strand371122
β-strand372-375420
β-strand378-379220
α-helix385-39410
β-strand399-403520

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Serine/threonine-protein kinase mTORAprotein2571Homo sapiensP42345 (AlphaFold model)
Target of rapamycin complex subunit LST8Cprotein326Homo sapiensQ9BVC4 (AlphaFold model)
Rapamycin-insensitive companion of mTOREprotein1708Homo sapiensQ6R327 (AlphaFold model)
Target of rapamycin complex 2 subunit MAPKAP1Gprotein522Homo sapiensQ9BPZ7 (AlphaFold model)
DEP domain-containing mTOR-interacting proteinIprotein409Homo sapiensQ8TB45
Sequence of entity 1 (A), FASTA
>7PE9_1 Serine/threonine-protein kinase mTOR (chains A)
MLGTGPAAATTAATTSSNVSVLQQFASGLKSRNEETRAKAAKELQHYVTMELREMSQEES
TRFYDQLNHHIFELVSSSDANERKGGILAIASLIGVEGGNATRIGRFANYLRNLLPSNDP
VVMEMASKAIGRLAMAGDTFTAEYVEFEVKRALEWLGADRNEGRRHAAVLVLRELAISVP
TFFFQQVQPFFDNIFVAVWDPKQAIREGAVAALRACLILTTQREPKEMQKPQWYRHTFEE
AEKGFDETLAKEKGMNRDGSTSGSGDYKDDDDKGSTSGSGDRIHGALLILNELVRISSME
GERLREEMEEITQQQLVHDKYCKDLMGFGTKPRHITPFTSFQAVQPQQSNALVGLLGYSS
HQGLMGFGTSPSPAKSTLVESRCCRDLMEEKFDQVCQWVLKCRNSKNSLIQMTILNLLPR
LAAFRPSAFTDTQYLQDTMNHVLSCVKKEKERTAAFQALGLLSVAVRSEFKVYLPRVLDI
IRAALPPKDFAHKRQKAMQVDATVFTCISMLARAMGPGIQQDIKELLEPMLAVGLSPALT
AVLYDLSRQIPQLKKDIQDGLLKMLSLVLMHKPLRHPGMPKGLAHQLASPGLTTLPEASD
VGSITLALRTLGSFEFEGHSLTQFVRHCADHFLNSEHKEIRMEAARTCSRLLTPSIHLIS
GHAHVVSQTAVQVVADVLSKLLVVGITDPDPDIRYCVLASLDERFDAHLAQAENLQALFV
ALNDQVFEIRELAICTVGRLSSMNPAFVMPFLRKMLIQILTELEHSGIGRIKEQSARMLG
HLVSNAPRLIRPYMEPILKALILKLKDPDPDPNPGVINNVLATIGELAQVSGLEMRKWVD
ELFIIIMDMLQDSSLLAKRQVALWTLGQLVASTGYVVEPYRKYPTLLEVLLNFLKTEQNQ
GTRREAIRVLGLLGALDPYKHKVNIGMIDQSRDASAVSLSESKSSQDSSDYSTSEMLVNM
GNLPLDEFYPAVSMVALMRIFRDQSLSHHHTMVVQAITFIFKSLGLKCVQFLPQVMPTFL
NVIRVCDGAIREFLFQQLGMLVSFVKSHIRPYMDEIVTLMREFWVMNTSIQSTIILLIEQ
IVVALGGEFKLYLPQLIPHMLRVFMHDNSPGRIVSIKLLAAIQLFGANLDDYLHLLLPPI
VKLFDAPEAPLPSRKAALETVDRLTESLDFTDYASRIIHPIVRTLDQSPELRSTAMDTLS
SLVFQLGKKYQIFIPMVNKVLVRHRINHQRYDVLICRIVKGYTLADEEEDPLIYQHRMLR
SGQGDALASGPVETGPMKKLHVSTINLQKAWGAARRVSKDDWLEWLRRLSLELLKDSSSP
SLRSCWALAQAYNPMARDLFNAAFVSCWSELNEDQQDELIRSIELALTSQDIAEVTQTLL
NLAEFMEHSDKGPLPLRDDNGIVLLGERAAKCRAYAKALHYKELEFQKGPTPAILESLIS
INNKLQQPEAAAGVLEYAMKHFGELEIQATWYEKLHEWEDALVAYDKKMDTNKDDPELML
GRMRCLEALGEWGQLHQQCCEKWTLVNDETQAKMARMAAAAAWGLGQWDSMEEYTCMIPR
DTHDGAFYRAVLALHQDLFSLAQQCIDKARDLLDAELTAMAGESYSRAYGAMVSCHMLSE
LEEVIQYKLVPERREIIRQIWWERLQGCQRIVEDWQKILMVRSLVVSPHEDMRTWLKYAS
LCGKSGRLALAHKTLVLLLGVDPSRQLDHPLPTVHPQVTYAYMKNMWKSARKIDAFQHMQ
HFVQTMQQQAQHAIATEDQQHKQELHKLMARCFLKLGEWQLNLQGINESTIPKVLQYYSA
ATEHDRSWYKAWHAWAVMNFEAVLHYKHQNQARDEKKKLRHASGANITNATTAATTAATA
TTTASTEGSNSESEAESTENSPTPSPLQKKVTEDLSKTLLMYTVPAVQGFFRSISLSRGN
NLQDTLRVLTLWFDYGHWPDVNEALVEGVKAIQIDTWLQVIPQLIARIDTPRPLVGRLIH
QLLTDIGRYHPQALIYPLTVASKSTTTARHNAANKILKNMCEHSNTLVQQAMMVSEELIR
VAILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDL
MEAQEWCRKYMKSGNVKDLTQAWDLYYHVFRRISKQLPQLTSLELQYVSPKLLMCRDLEL
AVPGTYDPNQPIIRIQSIAPSLQVITSKQRPRKLTLMGSNGHEFVFLLKGHEDLRQDERV
MQLFGLVNTLLANDPTSLRKNLSIQRYAVIPLSTNSGLIGWVPHCDTLHALIRDYREKKK
ILLNIEHRIMLRMAPDYDHLTLMQKVEVFEHAVNNTAGDDLAKLLWLKSPSSEVWFDRRT
NYTRSLAVMSMVGYILGLGDRHPSNLMLDRLSGKILHIDFGDCFEVAMTREKFPEKIPFR
LTRMLTNAMEVTGLDGNYRITCHTVMEVLREHKDSVMAVLEAFVYDPLLNWRLMDTNTKG
NKRSRTRTDSYSAGQSVEILDGVELGEPAHKKTGTTVPESIHSFIGDGLVKPEALNKKAI
QIINRVRDKLTGRDFSHDDTLDVPTQVELLIKQATSHENLCQCYIGWCPFW
Sequence of entity 2 (C), FASTA
>7PE9_2 Target of rapamycin complex subunit LST8 (chains C)
MNTSPGTVGSDPVILATAGYDHTVRFWQAHSGICTRTVQHQDSQVNALEVTPDRSMIAAA
GYQHIRMYDLNSNNPNPIISYDGVNKNIASVGFHEDGRWMYTGGEDCTARIWDLRSRNLQ
CQRIFQVNAPINCVCLHPNQAELIVGDQSGAIHIWDLKTDHNEQLIPEPEVSITSAHIDP
DASYMAAVNSTGNCYVWNLTGGIGDEVTQLIPKTKIPAHTRYALQCRFSPDSTLLATCSA
DQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVE
TGEIKREYGGHQKAVVCLAFNDSVLG
Sequence of entity 3 (E), FASTA
>7PE9_3 Rapamycin-insensitive companion of mTOR (chains E)
MAAIGRGRSLKNLRVRGRNDSGEENVPLDLTREPSDNLREILQNVARLQGVSNMRKLGHL
NNFTKLLCDIGHSEEKLGFHYEDIIICLRLALLNEAKEVRAAGLRALRYLIQDSSILQKV
LKLKVDYLIARCIDIQQSNEVERTQALRLVRKMITVNASLFPSSVTNSLIAVGNDGLQER
DRMVRACIAIICELALQNPEVVALRGGLNTILKNVIDCQLSRINEALITTILHLLNHPKT
RQYVRADVELERILAPYTDFHYRHSPDTAEGQLKEDREARFLASKMGIIATFRSWAGIIN
LCKPGNSGIQSLIGVLCIPNMEIRRGLLEVLYDIFRLPLPVVTEEFIEALLSVDPGRFQD
SWRLSDGFVAAEAKTILPHRARSRPDLMDNYLALILSAFIRNGLLEGLVEVITNSDDHIS
VRATILLGELLHMANTILPHSHSHHLHCLPTLMNMAASFDIPKEKRLRASAALNCLKRFH
EMKKRGPKPYSLHLDHIIQKAIATHQKRDQYLRVQKDIFILKDTEEALLINLRDSQVLQH
KENLEWNWNLIGTILKWPNVNLRNYKDEQLHRFVRRLLYFYKPSSKLYANLDLDFAKAKQ
LTVVGCQFTEFLLESEEDGQGYLEDLVKDIVQWLNASSGMKPERSLQNNGLLTTLSQHYF
LFIGTLSCHPHGVKMLEKCSVFQCLLNLCSLKNQDHLLKLTVSSLDYSRDGLARVILSKI
LTAATDACRLYATKHLRVLLRANVEFFNNWGIELLVTQLHDKNKTISSEALDILDEACED
KANLHALIQMKPALSHLGDKGLLLLLRFLSIPKGFSYLNERGYVAKQLEKWHREYNSKYV
DLIEEQLNEALTTYRKPVDGDNYVRRSNQRLQRPHVYLPIHLYGQLVHHKTGCHLLEVQN
IITELCRNVRTPDLDKWEEIKKLKASLWALGNIGSSNWGLNLLQEENVIPDILKLAKQCE
VLSIRGTCVYVLGLIAKTKQGCDILKCHNWDAVRHSRKHLWPVVPDDVEQLCNELSSIPS
TLSLNSESTSSRHNSESESVPSSMFILEDDRFGSSSTSTFFLDINEDTEPTFYDRSGPIK
DKNSFPFFASSKLVKNRILNSLTLPNKKHRSSSDPKGGKLSSESKTSNRRIRTLTEPSVD
FNHSDDFTPISTVQKTLQLETSFMGNKHIEDTGSTPSIGENDLKFTKNFGTENHRENTSR
ERLVVESSTSSHMKIRSQSFNTDTTTSGISSMSSSPSRETVGVDATTMDTDCGSMSTVVS
TKTIKTSHYLTPQSNHLSLSKSNSVSLVPPGSSHTLPRRAQSLKAPSIATIKSLADCNFS
YTSSRDAFGYATLKRLQQQRMHPSLSHSEALASPAKDVLFTDTITMKANSFESRLTPSRF
MKALSYASLDKEDLLSPINQNTLQRSSSVRSMVSSATYGGSDDYIGLALPVDINDIFQVK
DIPYFQTKNIPPHDDRGARAFAHDAGGLPSGTGGLVKNSFHLLRQQMSLTEIMNSIHSDA
SLFLESTEDTGLQEHTDDNCLYCVCIEILGFQPSNQLSAICSHSDFQDIPYSDWCEQTIH
NPLEVVPSKFSGISGCSDGVSQEGSASSTKSTELLLGVKTIPDDTPMCRILLRKEVLRLV
INLSSSVSTKCHETGLLTIKEKYPQTFDDICLYSEVSHLLSHCTFRLPCRRFIQELFQDV
QFLQMHEEAEAVLATPPKQPIVDTSAES
Sequence of entity 4 (G), FASTA
>7PE9_4 Target of rapamycin complex 2 subunit MAPKAP1 (chains G)
MAFLDNPTIILAHIRQSHVTSDDTGMCEMVLIDHDVDLEKIHPPSMPGDSGSEIQGSNGE
TQGYVYAQSVDITSSWDFGIRRRSNTAQRLERLRKERQNQIKCKNIQWKERNSKQSAQEL
KSLFEKKSLKEKPPISGKQSILSVRLEQCPLQLNNPFNEYSKFDGKGHVGTTATKKIDVY
LPLHSSQDRLLPMTVVTMASARVQDLIGLICWQYTSEGREPKLNDNVSAYCLHIAEDDGE
VDTDFPPLDSNEPIHKFGFSTLALVEKYSSPGLTSKESLFVRINAAHGFSLIQVDNTKVT
MKEILLKAVKRRKGSQKVSGPQYRLEKQSEPNVAVDLDSTLESQSAWEFCLVRENSSRAD
GVFEEDSQIDIATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKAS
TKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVL
KVNYILESRASTARADYFAQKQRKLNRRTSFSFQKEKKSGQQ
Sequence of entity 5 (I), FASTA
>7PE9_5 DEP domain-containing mTOR-interacting protein (chains I)
MEEGGSTGSAGSDSSTSGSGGAQQRELERMAEVLVTGEQLRLRLHEEKVIKDRRHHLKTY
PNCFVAKELIDWLIEHKEASDRETAIKLMQKLADRGIIHHVCDEHKEFKDVKLFYRFRKD
DGTFPLDNEVKAFMRGQRLYEKLMSPENTLLQPREEEGVKYERTFMASEFLDWLVQEGEA
TTRKEAEQLCHRLMEHGIIQHVSSKHPFVDSNLLYQFRMNFRRRRRLMELLNEKSPSSQE
THDSPFCLRKQSHDNRKSTSFMSVSPSKEIKIVSAVRRSSMSSCGSSGYFSSSPTLSSSP
PVLCNPKSVLKRPVTSEELLTPGAPYARKTFTIVGDAVGWGFVVRGSKPCHIQAVDPSGP
AAAAGMKVCQFVVSVNGLNVLHVDYRTVNNLILTGPRTIVMEVMEELEC

Ligands and cofactors

IDNameFormulaCopies
ACEAcetyl groupC2 H4 O1
ZNZinc ionZn1
IHPInositol hexakisphosphateC6 H18 O24 P61

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:

Browse structure collections

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