9CE3: TSC:WIPI3 lysosomal recruitment complex

Structure of the TSC:WIPI3 lysosomal recruitment complex. Determined by electron microscopy at 2.9 Å resolution. Released 4 Dec 2024.

Method
Electron microscopy
Resolution
2.9 Å
Organism
Homo sapiens
Chains
8
Atoms
35,086
Mol. weight
737 kDa
Released
4 Dec 2024

Explore 9CE3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CE3 contains 245 α-helices and 83 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: 79 helices, 21 β-strands

ElementResiduesLengthSheet
α-helix42-487
α-helix54-7017
α-helix75-8612
α-helix95-11218
α-helix113-1153
α-helix119-12810
α-helix136-14712
α-helix148-1503
α-helix160-17011
α-helix174-18613
α-helix189-1946
α-helix195-20814
α-helix212-22817
α-helix233-2353
α-helix236-24611
α-helix250-2523
α-helix253-26412
α-helix269-28113
α-helix283-2853
α-helix289-30416
α-helix316-3183
α-helix320-3267
α-helix332-34918
α-helix355-37117
α-helix378-39619
α-helix404-41310
α-helix415-4173
α-helix420-43213
α-helix441-4499
α-helix450-4545
α-helix459-47618
α-helix481-4844
α-helix485-4895
α-helix490-4934
α-helix496-4983
α-helix502-51817
α-helix524-53512
α-helix549-5546
α-helix555-5573
α-helix558-57417
α-helix581-60020
α-helix605-61814
β-strand622-62321
β-strand628-63251
β-strand638-64581
β-strand682-68321
α-helix686-69914
β-strand70212
α-helix703-71715
α-helix720-7256
α-helix730-74213
α-helix745-7495
β-strand75112
α-helix759-77315
α-helix774-7796
α-helix782-79413
α-helix795-7973
α-helix801-81414
α-helix816-83116
α-helix837-85115
α-helix862-87211
α-helix873-8764
α-helix883-89917
α-helix902-9054
α-helix908-92114
α-helix934-9363
α-helix1005-103329
β-strand103813
α-helix1046-10527
β-strand1056-106164
β-strand1066-107164
α-helix1077-10815
α-helix1186-11916
β-strand1194-120184
β-strand1204-121294
α-helix1214-12152
β-strand121615
α-helix12171
α-helix1229-12324
α-helix1236-12383
α-helix1497-15059
β-strand1518-151924
α-helix1525-153612
β-strand1541-1550106
α-helix1558-15636
α-helix1569-15768
β-strand1580-158346
α-helix1584-15863
β-strand1606-161166
β-strand1615-162176
α-helix1622-16243
α-helix1635-16417
β-strand1646-165166
β-strand1669-167686
β-strand1680-168786
α-helix1691-16933
β-strand1700-170456
α-helix1708-173023
α-helix1735-17362
α-helix1739-176022
Chain B: 77 helices, 23 β-strands
ElementResiduesLengthSheet
α-helix42-443
α-helix45-484
α-helix54-6815
β-strand7117
α-helix73-742
α-helix77-859
α-helix86-883
α-helix95-11117
α-helix113-1153
α-helix118-12811
α-helix137-14711
α-helix148-1503
α-helix157-17014
α-helix174-18714
α-helix188-1903
α-helix192-1943
α-helix195-20612
α-helix212-22716
α-helix236-24611
α-helix250-2523
α-helix253-26412
α-helix268-28114
α-helix283-2853
α-helix289-30416
α-helix316-32510
α-helix334-34815
α-helix355-37521
α-helix378-39619
α-helix404-41310
α-helix421-43111
α-helix441-45212
α-helix459-47618
α-helix481-4844
α-helix485-4895
α-helix490-4912
α-helix493-4953
α-helix502-51817
α-helix524-53613
α-helix541-5422
α-helix547-57428
α-helix581-60020
α-helix605-61814
β-strand622-62328
β-strand628-63258
β-strand638-64588
α-helix679-6813
β-strand682-68328
α-helix686-69914
β-strand70219
α-helix703-71614
α-helix720-7245
α-helix730-74213
α-helix746-7494
β-strand75119
α-helix753-7542
α-helix759-77315
α-helix774-7763
α-helix782-79413
α-helix795-7973
α-helix801-81414
α-helix816-83116
α-helix837-85115
α-helix862-87211
α-helix873-8764
α-helix883-89917
α-helix902-92019
α-helix933-9364
α-helix1005-103329
β-strand103815
α-helix1046-10527
β-strand1056-106164
β-strand1066-107164
α-helix1075-10817
α-helix1183-11853
β-strand1194-120184
β-strand1204-121294
α-helix12151
β-strand121613
α-helix1228-123710
α-helix1497-15059
α-helix1513-15153
β-strand1518-151924
α-helix1525-153612
β-strand1541-15501010
α-helix1558-15625
α-helix1569-15768
β-strand1580-1583410
α-helix1584-15863
β-strand1606-1611610
β-strand1615-1621710
α-helix1626-16272
α-helix1635-16417
β-strand1646-1651610
β-strand1669-1676810
β-strand1680-1683410
β-strand1686-1687210
β-strand1701-1704410
α-helix1708-173023
α-helix1735-17362
α-helix1739-176123
Chain C: 30 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix7-126
β-strand1817
α-helix19-3517
α-helix40-5213
α-helix55-628
α-helix68-8114
α-helix86-9813
α-helix102-1087
α-helix112-12110
α-helix126-13914
α-helix144-1463
α-helix147-16721
α-helix174-19421
α-helix196-20712
α-helix213-2153
α-helix216-2205
α-helix221-2244
β-strand227111
β-strand228112
α-helix229-2302
α-helix232-2354
α-helix238-2425
α-helix244-2474
α-helix252-2609
β-strand263111
α-helix605-6117
α-helix613-6197
α-helix656-6627
α-helix669-6735
α-helix676-6783
α-helix685-793109
α-helix795-86672
α-helix869-8735
α-helix874-96996
Chain D: 36 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix7-148
α-helix19-3517
α-helix40-5213
α-helix55-628
α-helix68-8114
α-helix86-9813
α-helix104-1085
α-helix112-12211
α-helix126-13914
α-helix144-1463
α-helix147-16721
α-helix174-19421
α-helix196-20712
α-helix210-2123
α-helix213-2153
α-helix216-2205
α-helix221-2233
α-helix224-2263
β-strand227113
β-strand228112
α-helix232-2354
α-helix239-2413
α-helix244-2485
α-helix252-26110
β-strand263113
α-helix616-63116
α-helix646-66621
α-helix689-72739
α-helix731-74111
α-helix744-77532
α-helix776-7805
α-helix781-7833
α-helix784-7918
α-helix792-80312
α-helix804-8096
α-helix810-83021
α-helix841-86626
α-helix869-8713
α-helix875-96793
Chain E: 19 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix20-3314
β-strand36114
α-helix39-4810
α-helix50-523
α-helix53-6311
β-strand70114
α-helix71-733
α-helix74-9421
α-helix104-11512
α-helix126-1283
α-helix129-14416
α-helix148-16316
α-helix169-19426
α-helix198-2003
α-helix2031
α-helix204-2085
β-strand212115
β-strand215115
α-helix217-22812
α-helix233-24513
α-helix247-2504
α-helix256-2649
α-helix271-28515
Chain F: 4 helices, 28 β-strands
ElementResiduesLengthSheet
β-strand13-18616
β-strand24-29616
β-strand32-37616
β-strand42-48716
β-strand56-58317
β-strand65-69517
β-strand75-80617
β-strand85-91717
α-helix951
β-strand96-102718
β-strand105-110618
β-strand113-118618
β-strand125-130618
β-strand140-141219
β-strand149-153519
β-strand160-164519
α-helix171-1722
β-strand173-175319
β-strand182-187620
β-strand193-198620
β-strand203-208620
β-strand214-219620
β-strand229-232421
β-strand238-243621
α-helix244-2463
β-strand247-252621
β-strand263-266421
β-strand273-277522
β-strand283-288622
β-strand292-298722
β-strand304-311822
α-helix312-3143

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Isoform 4 of TuberinA, Bprotein1792Homo sapiensP49815 (AlphaFold model)
HamartinC, Dprotein1191Homo sapiensQ92574 (AlphaFold model)
TBC1 domain family member 7Eprotein301Homo sapiensQ9P0N9 (AlphaFold model)
WD repeat domain phosphoinositide-interacting protein 3Fprotein316Homo sapiensQ5MNZ6 (AlphaFold model)
Unknown fragmentG, Hprotein12Homo sapiens
Sequence of entity 1 (A, B), FASTA
>9CE3_1 Isoform 4 of Tuberin (chains A, B)
MDYKDDDDKAKPTSKDSGLKEKFKILLGLGTPRPNPRSAEGKQTEFIITAEILRELSMEC
GLNNRIRMIGQICEVAKTKKFEEHAVEALWKAVADLLQPERPLEARHAVLALLKAIVQGQ
GERLGVLRALFFKVIKDYPSNEDLHERLEVFKALTDNGRHITYLEEELADFVLQWMDVGL
SSEFLLVLVNLVKFNSCYLDEYIARMVQMICLLCVRTASSVDIEVSLQVLDAVVCYNCLP
AESLPLFIVTLCRTINVKELCEPCWKLMRNLLGTHLGHSAIYNMCHLMEDRAYMEDAPLL
RGAVFFVGMALWGAHRLYSLRNSPTSVLPSFYQAMACPNEVVSYEIVLSITRLIKKYRKE
LQVVAWDILLNIIERLLQQLQTLDSPELRTIVHDLLTTVEELCDQNEFHGSQERYFELVE
RCADQRPESSLLNLISYRAQSIHPAKDGWIQNLQALMERFFRSESRGAVRIKVLDVLSFV
LLINRQFYEEELINSVVISQLSHIPEDKDHQVRKLATQLLVDLAEGCHTHHFNSLLDIIE
KVMARSLSPPPELEERDVAAYSASLEDVKTAVLGLLVILQTKLYTLPASHATRVYEMLVS
HIQLHYKHSYTLPIASSIRLQAFDFLLLLRADSLHRLGLPNKDGVVRFSPYCVCDYMEPE
RGSEKKTSGPLSPPTGPPGPAPAGPAVRLGSVPYSLLFRVLLQCLKQESDWKVLKLVLGR
LPESLRYKVLIFTSPCSVDQLCSALCSMLSGPKTLERLRGAPEGFSRTDLHLAVVPVLTA
LISYHNYLDKTKQREMVYCLEQGLIHRCASQCVVALSICSVEMPDIIIKALPVLVVKLTH
ISATASMAVPLLEFLSTLARLPHLYRNFAAEQYASVFAISLPYTNPSKFNQYIVCLAHHV
IAMWFIRCRLPFRKDFVPFITKGLRSNVLLSFDDTPEKDSFRARSTSLNERPKSLRIARP
PKQGLNNSPPVKEFKESSAAEAFRCRSISVSEHVVRSRIQTSLTSASLGSADENSVAQAD
DSLKNLHLELTETCLDMMARYVFSNFTAVPKRSPVGEFLLAGGRTKTWLVGNKLVTVTTS
VGTGTRSLLGLDSGELQSGPESSSSPGVHVRQTKEAPAKLESQAGQQVSRGARDRVRSMS
GGHGLRVGALDVPASQFLGSATSPGPRTAPAAKPEKASAGTRVPVQEKTNLAAYVPLLTQ
GWAEILVRRPTGNTSWLMSLENPLSPFSSDINNMPLQELSNALMAAERFKEHRDTALYKS
LSVPAASTAKPPPLPRSNTDSAVVMEEGSPGEVPVLVEPPGLEDVEAALGMDRRTDAYSR
SSSVSSQEEKSLHAEELVGRGIPIERVVSSEGGRPSVDLSFQPSQPLSKSSSSPELQTLQ
DILGDPGDKADVGRLSPEVKARSQSGTLDGESAAWSASGEDSRGQPEGPLPSSSPRSPSG
LRPRGYTISDSAPSRRGKRVERDALKSRATASNAEKVPGINPSFVFLQLYHSPFFGDESN
KPILLPNESQSFERSVQLLDQIPSYDTHKIAVLYVGEGQSNSELAILSNEHGSYRYTEFL
TGLGRLIELKDCQPDKVYLGGLDVCGEDGQFTYCWHDDIMQAVFHIATLMPTKDVDKHRC
DKKRHLGNDFVSIVYNDSGEDFKLGTIKGQFNFVHVIVTPLDYECNLVSLQCRKDMEGLV
DTSVAKIVSDRNLPFVARQMALHANMASQVHHSRSNPTDIYPSKWIARLRHIKRLRQRIC
EEAAYSNPSLPLVHPPSHSKAPAQTPAEPTPGYEVGQRKRLISSVEDFTEFV
Sequence of entity 2 (C, D), FASTA
>9CE3_2 Hamartin (chains C, D)
MAQQANVGELLAMLDSPMLGVRDDVTAVFKENLNSDRGPMLVNTLVDYYLETSSQPALHI
LTTLQEPHDKHLLDRINEYVGKAATRLSILSLLGHVIRLQPSWKHKLSQAPLLPSLLKCL
KMDTDVVVLTTGVLVLITMLPMIPQSGKQHLLDFFDIFGRLSSWCLKKPGHVAEVYLVHL
HASVYALFHRLYGMYPCNFVSFLRSHYSMKENLETFEEVVKPMMEHVRIHPELVTGSKDH
ELDPRRWKRLETHDVVIECAKISLDPTEASYEDGYSVSHQISARFPHRSADVTTSPYADT
QNSYGCATSTPYSTSRLMLLNMPGQLPQTLSSPSTRLITEPPQATLWSPSMVCGMTTPPT
SPGNVPPDLSHPYSKVFGTTAGGKGTPLGTPATSPPPAPLCHSDDYVHISLPQATVTPPR
KEERMDSARPCLHRQHHLLNDRGSEEPPGSKGSVTLSDLPGFLGDLASEEDSIEKDKEEA
AISRELSEITTAEAEPVVPRGGFDSPFYRDSLPGSQRKTHSAASSSQGASVNPEPLHSSL
DKLGPDTPKQAFTPIDLPCGSADESPAGDRECQTSLETSIFTPSPCKIPPPTRVGFGSGQ
PPPYDHLFEVALPKTAHHFVIRKTEELLKKAKGNTEEDGVPSTSPMEVLDRLIQQGADAH
SKELNKLPLPSKSVDWTHFGGSPPSDEIRTLRDQLLLLHNQLLYERFKRQQHALRNRRLL
RKVIKAAALEEHNAAMKDQLKLQEKDIQMWKVSLQKEQARYNQLQEQRDTMVTKLHSQIR
QLQHDREEFYNQSQELQTKLEDCRNMIAELRIELKKANNKVCHTELLLSQVSQKLSNSES
VQQQMEFLNRQLLVLGEVNELYLEQLQNKHSDTTKEVEMMKAAYRKELEKNRSHVLQQTQ
RLDTSQKRILELESHLAKKDHLLLEQKKYLEDVKLQARGQLQAAESRYEAQKRITQVFEL
EILDLYGRLEKDGLLKKLEEEKAEAAEAAEERLDCCNDGCSDSMVGHNEEASGHNGETKT
PRPSSARGSSGSRGGGGSSSSSSELSTPEKPPHQRAGPFSSRWETTMGEASASIPTTVGS
LPSSKSFLGMKARELFRNKSESQCDEDGMTSSLSESLKTELGKDLGVEAKIPLNLDGPHP
SPPTPDSVGQLHIMDYNETHHEHSGTKLGPEQKLISEEDLNSAVDHHHHHH
Sequence of entity 3 (E), FASTA
>9CE3_3 TBC1 domain family member 7 (chains E)
MTEDSQRNFRSVYYEKVGFRGVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVW
KVLLGILPPHHESHAKVMMYRKEQYLDVLHALKVVRFVSDATPQAEVYLRMYQLESGKLP
RSPSFPLEPDDEVFLAIAKAMEEMVEDSVDCYWITRRFVNQLNTKYRDSLPQLPKAFEQY
LNLEDGRLLTHLRMCSAAPKLPYDLWFKRCFAGCLPESSLQRVWDKVVSGSCKILVFVAV
EILLTFKIKVMALNSAEKITKFLENIPQDSSDAIVSKAIDLWHKHCGTPVHSSDYKDDDD
K
Sequence of entity 4 (F), FASTA
>9CE3_4 WD repeat domain phosphoinositide-interacting protein 3 (chains F)
MHHHHHHGLLYAGFNQDHGCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCN
YLALVGGGKKKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPH
QLHVFETCYNPKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSC
IALNLQGTRIATASEKGTLIRIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSD
HGTVHIFAAEDPKSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGSYYKFLFNPKGEC
IRDVYAQFLEMTDDKL
Sequence of entity 5 (G, H), FASTA
>9CE3_5 Unknown fragment (chains G, H)
XXXXXXXXXXXX

Primary citation

Structure of the human TSC:WIPI3 lysosomal recruitment complex. Bayly-Jones, C., Lupton, C.J., D'Andrea, L. et al. Sci Adv (2024) 10:eadr5807-eadr5807. DOI 10.1126/sciadv.adr5807 · PubMed

Other PDB entries of the same protein (UniProt P49815 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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