9C82: Human ULK1C:PI3KC3-C1 supercomplex

Structure of human ULK1C:PI3KC3-C1 supercomplex. Determined by electron microscopy at 6.84 Å resolution. Released 3 Jul 2024.

Method: Electron microscopy
Resolution: 6.84 Å
Organism: Homo sapiens
Chains: 5
Atoms: 11,172
Mol. weight: 435.64 kDa
Released: 3 Jul 2024

Explore 9C82 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C82 contains 78 α-helices and 77 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: 42 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	65-78	14
β-strand	84	1	1
β-strand	108-109	2	1
α-helix	110-115	6
α-helix	122-142	21
β-strand	154-156	3	1
β-strand	163-164	2	1
α-helix	180-186	7
α-helix	199-201	3
α-helix	237-253	17
α-helix	261-269	9
α-helix	275-280	6
α-helix	284-293	10
α-helix	305-313	9
α-helix	320-331	12
α-helix	339-357	19
α-helix	373-386	14
α-helix	392-409	18
α-helix	413	1
α-helix	414-418	5
α-helix	419-425	7
α-helix	431-446	16
α-helix	453-469	17
α-helix	476-503	28
α-helix	527-544	18
α-helix	550-560	11
α-helix	562-565	4
α-helix	569-583	15
α-helix	591-608	18
α-helix	613-624	12
α-helix	629-645	17
α-helix	649-663	15
α-helix	669-685	17
α-helix	688-690	3
α-helix	691-695	5
α-helix	696-699	4
β-strand	703	1	2
α-helix	714-719	6
β-strand	720	1	2
α-helix	721-724	4
α-helix	726-734	9
α-helix	738-752	15
α-helix	764-778	15
α-helix	783-804	22
α-helix	974-976	3
β-strand	985-989	5	3
β-strand	998-1001	4	4
β-strand	1007-1012	6	4
β-strand	1016-1021	6	4
α-helix	1022-1025	4
β-strand	1037-1038	2	4
β-strand	1045-1050	6	5
β-strand	1057-1061	5	5
β-strand	1065-1069	5	5
α-helix	1071-1074	4
β-strand	1084-1089	6	5
β-strand	1100-1105	6	6
β-strand	1110-1116	7	6
β-strand	1120-1125	6	6
β-strand	1134-1135	2	6
β-strand	1146-1149	4	7
β-strand	1155-1159	5	7
β-strand	1164-1169	6	7
β-strand	1175-1180	6	7
β-strand	1191-1192	2	8
β-strand	1199-1204	6	8
β-strand	1209-1214	6	8
β-strand	1219-1220	2	8
β-strand	1224-1225	2	9
α-helix	1230	1
β-strand	1242-1250	9	10
β-strand	1253-1260	8	10
β-strand	1265-1268	4	10
β-strand	1290-1292	3	9
β-strand	1295	1	11
β-strand	1298	1	11
β-strand	1301-1303	3	9
β-strand	1335-1339	5	3
β-strand	1343-1348	6	3
β-strand	1354-1357	4	3

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	12
α-helix	12-15	4
α-helix	17-19	3
β-strand	21-23	3	13
α-helix	35-40	6
α-helix	44-46	3
α-helix	48-51	4
β-strand	58-65	8	14
β-strand	68-69	2	14
β-strand	74	1	14
β-strand	89-91	3	13
β-strand	104-113	10	14
β-strand	119-128	10	14
β-strand	130	1	15
β-strand	136	1	15
β-strand	140	1	16
β-strand	143-144	2	17
β-strand	149	1	14
β-strand	160	1	14
α-helix	171-183	13
α-helix	192-210	19
β-strand	216-217	2	17
β-strand	220	1	16
α-helix	221-223	3
β-strand	224	1	18
β-strand	229	1	18
β-strand	233-234	2	12

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	77-204	128
β-strand	209-210	2	19
β-strand	260-262	3	19
β-strand	269-271	3	19
α-helix	276-278	3
α-helix	299-320	22
α-helix	331-335	5
α-helix	342-361	20
α-helix	366-369	4
α-helix	374-382	9

Chain D: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	111-126	16
α-helix	134-136	3
α-helix	138-168	31
α-helix	172-266	95
α-helix	269-274	6
β-strand	277	1	20
β-strand	284	1	20
β-strand	293	1	21
β-strand	296	1	21
α-helix	300-320	21
β-strand	329-330	2	22
β-strand	337-338	2	23
β-strand	339-340	2	22
β-strand	341	1	24
β-strand	344	1	24
β-strand	350-351	2	23
α-helix	364-384	21
β-strand	395-397	3	25
β-strand	402-404	3	25
β-strand	414	1	25
α-helix	423-448	26

Chain F: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	26
β-strand	12-13	2	26
α-helix	18-20	3
α-helix	25-34	10
β-strand	44-46	3	26
α-helix	51-53	3
α-helix	59-62	4
β-strand	71-74	4	26
α-helix	76-80	5
α-helix	93-107	15
α-helix	115-201	87
α-helix	308-316	9
α-helix	321-334	14
α-helix	337-354	18
α-helix	357-360	4
α-helix	365-402	38
α-helix	412-491	80

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphoinositide 3-kinase regulatory subunit 4	A	protein	1358	Homo sapiens	Q99570 (AlphaFold model)
Phosphatidylinositol 3-kinase catalytic subunit type 3	B	protein	887	Homo sapiens	Q8NEB9 (AlphaFold model)
Beclin 1-associated autophagy-related key regulator	C	protein	492	Homo sapiens	O75385 (AlphaFold model)
Beclin-1	D	protein	450	Homo sapiens	O75143 (AlphaFold model)
RB1-inducible coiled-coil protein 1	F	protein	640	Homo sapiens	Q8TDY2

Sequence of entity 1 (A), FASTA

>9C82_1 Phosphoinositide 3-kinase regulatory subunit 4 (chains A)
MGNQLAGIAPSQILSVESYFSDIHDFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDP
TLPLTSYKQELEELKIRLNSAQNCLPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFL
NNIEKRWIAFQILTAVDQAHKSGVRHGDIKTENVMVTSWNWVLLTDFASFKPTYLPEDNP
ADFNYFFDTSRRRTCYIAPERFVDGGMFATELEYMRDPSTPLVDLNSNQRTRGELKRAMD
IFSAGCVIAELFTEGVPLFDLSQLLAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDK
RLEAEDYLKQQRGNAFPEIFYTFLQPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGH
DLPEKAEGEPKENGLVILVSVITSCLQTLKYCDSKLAALELILHLAPRLSVEILLDRITP
YLLHFSNDSVPRVRAEALRTLTKVLALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRL
AYAENIALLAETALRFLELVQLKNLNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQK
VVTLLSDPENIVKQTLMENGITRLCVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDS
IVGVAAYVGWQSSSILKPLLQQGLSDAEEFVIVKALYALTCMCQLGLLQKPHVYEFASDI
APFLCHPNLWIRYGAVGFITVVARQISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVL
KEPVSRSIFDYALRSKDITSLFRHLHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMT
EEEEDKLLALKDFMMKSNKAKANIVDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEP
DDKRARKHVKQDSNVNEEWKSMFGSLDPPNMPQALPKGSDQEVIQTGKPPRSESSAGICV
PLSTSSQVPEVTTVQNKKPVIPVLSSTILPSTYQIRITTCKTELQQLIQQKREQCNAERI
AKQMMENAEWESKPPPPGWRPKGLLVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIW
NSQKMEGKTTTTRSILTYSRIGGRVKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSP
KIHPLQSRILDQKEDGCVVDMHHFNSGAQSVLAYATVNGSLVGWDLRSSSNAWTLKHDLK
SGLITSFAVDIHQCWLCIGTSSGTMACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWV
IAAVQGNNEVSMWDMETGDRRFTLWASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAG
SDMKIRFWDLAYPERSYVVAGSTSSPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRG
PESLPVGHHDIITDVATFQTTQGFIVTASRDGIVKVWK

Sequence of entity 2 (B), FASTA

>9C82_2 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains B)
MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLYVT
CQVFAEGKPLALPVRTSYKAFSTRWNWNEWLKLPVKYPDLPRNAQVALTIWDVYGPGKAV
PVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTPGRTSSTLSEDQMSRLAKLTK
AHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYGIVYYEKDG
DESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNAATRDQLNIIV
SYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDV
EDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKK
DSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLI
SRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRS
LLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVK
IRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRK
ENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAE
VMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLN
KEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVK
KVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIHKFAQYWRK

Sequence of entity 3 (C), FASTA

>9C82_3 Beclin 1-associated autophagy-related key regulator (chains C)
MASPSGKGARALEAPGCGPRPLARDLVDSVDDAEGLYVAVERCPLCNTTRRRLTCAKCVQ
SGDFVYFDGRDRERFIDKKERLSRLKSKQEEFQKEVLKAMEGKWITDQLRWKIMSCKMRI
EQLKQTICKGNEEMEKNSEGLLKTKEKNQKLYSRAQRHQEKKEKIQRHNRKLGDLVEKKT
IDLRSHYERLANLRRSHILELTSVIFPIEEVKTGVRDPADVSSESDSAMTSSTVSKLAEA
RRTTYLSGRWVCDDHNGDTSISITGPWISLPNNGDYSAYYSWVEEKKTTQGPDMEQSNPA
YTISAALCYATQLVNILSHILDVNLPKKLCNSEFCGENLSKQKFTRAVKKLNANILYLCF
SQHVNLDQLQPLHTLRNLMYLVSPSSEHLGRSGPFEVRADLEESMEFVDPGVAGESDESG
DERVSDEETDLGTDWENLPSPRFCDIPSQSVEVSQSQSTQASPPIASSSAGGMISSAAAS
VTSWFKAYTGHR

Sequence of entity 4 (D), FASTA

>9C82_4 Beclin-1 (chains D)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Sequence of entity 5 (F), FASTA

>9C82_5 RB1-inducible coiled-coil protein 1 (chains F)
MKLYVFLVNTGTTLTFDTELTVQTVADLKHAIQSKYKIAIQHQVLVVNGGECMAADRRVC
TYSAGTDTNPIFLFNKEMILCDRPPAIPKTTFSTENDMEIKVEESLMMPAVFHTVASRTQ
LALEMYEVAKKLCSFCEGLVHDEHLQHQGWAAIMANLEDCSNSYQKLLFKFESIYSNYLQ
SIEDIKLKLTHLGTAVSVMAKIPLLECLTRHSYRECLGRLDSLPEHEDSEKAEMKRSTEL
VLSPDMPRTTNESLLTSFPKSVEHVSPDTADAESGKEIRESCQSTVHQQDETTIDTKDGD
LPFFNVSLLDWINVQDRPNDVESLVRKCFDSMSRLDPRIIRPFIAECRQTIAKLDNQNMK
AIKGLEDRLYALDQMIASCGRLVNEQKELAQGFLANQKRAENLKDASVLPDLCLSHANQL
MIMLQNHRKLLDIKQKCTTAKQELANNLHVRLKWCCFVMLHADQDGEKLQALLRLVIELL
ERVKIVEALSTVPQMYCLAVVEVVRRKMFIKHYREWAGALVKDGKRLYEAEKSKRESFGK
LFRKSFLRNRLFRGLDSWPPSFCTQKPRKFDCELPDISLKDLQFLQSFCPSEVQPFLRVP
LLCDFEPLHQHVLALHNLVKAAQSLDEMSQTITDLLSEQK

Primary citation

Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex. Chen, M., Nguyen, T.N., Ren, X. et al. Nat Struct Mol Biol (2025) 32:1596-1605. DOI 10.1038/s41594-025-01557-x · PubMed

Other PDB entries of the same protein (UniProt Q99570 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9MHF 2.73 Å, Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L)
9RX5 3.15 Å, VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L)
9MHG 3.2 Å, Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase…
9RX7 3.33 Å, VPS34-CI bound to NRBF2 MIT domain (residues 1-79)
9RX6 3.52 Å, VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15…
9TW2 3.58 Å, Cryo-EM structure of human VPS34-CI in complex with GABARAP
9TW3 3.6 Å, Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation
9TZ3 3.66 Å, Cryo-EM structure of human VPS34-CI with ADP:MgF3
9RX4 3.67 Å, VPS34-CI bound to NRBF2 and RAB1A
13BV 3.77 Å, Cryo-EM structure of human PI3KC3-C1 complex
9RX8 3.87 Å, Apo VPS34-cii (VPS34/VPS15/BECLIN1/UVRAG)
9RX9 3.99 Å, VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit

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