13BV: Human PI3KC3-C1 complex

Cryo-EM structure of human PI3KC3-C1 complex. Determined by electron microscopy at 3.77 Å resolution. Released 13 May 2026.

Method: Electron microscopy
Resolution: 3.77 Å
Organism: Homo sapiens
Chains: 4
Atoms: 15,991
Mol. weight: 363.01 kDa
Ligands: MG, GDP, MYR
Released: 13 May 2026

Explore 13BV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

13BV contains 81 α-helices and 79 β-strands across 4 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: 61 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	16-23	8
β-strand	33-34	2	10
β-strand	39-44	6	10
β-strand	49-54	6	10
α-helix	65-77	13
α-helix	78-80	3
β-strand	84-85	2	11
β-strand	89-91	3	10
β-strand	100-104	5	10
α-helix	105-106	2
β-strand	108-109	2	11
α-helix	110-115	6
α-helix	119	1
α-helix	122-141	20
β-strand	154-156	3	11
β-strand	162-165	4	11
β-strand	175-176	2	12
α-helix	181-186	6
α-helix	199-201	3
β-strand	202-203	2	12
α-helix	237-252	16
α-helix	261-269	9
α-helix	275-279	5
α-helix	284-294	11
α-helix	304-310	7
β-strand	312	1	13
β-strand	316	1	13
α-helix	318-319	2
α-helix	320-324	5
α-helix	325-329	5
α-helix	339-357	19
α-helix	375-386	12
α-helix	392-405	14
α-helix	406-408	3
α-helix	411-413	3
α-helix	414-418	5
α-helix	419-425	7
α-helix	431-446	16
α-helix	454-457	4
α-helix	458	1
α-helix	459-463	5
α-helix	464-467	4
α-helix	476-503	28
α-helix	527-545	19
α-helix	550-559	10
α-helix	565-568	4
α-helix	570-572	3
α-helix	573-577	5
α-helix	578-584	7
α-helix	591-608	18
α-helix	610-612	3
α-helix	613-623	11
α-helix	629-644	16
α-helix	650-660	11
α-helix	661-665	5
α-helix	669-685	17
α-helix	688-690	3
α-helix	691-695	5
α-helix	696-699	4
α-helix	713-719	7
α-helix	720-725	6
α-helix	726-734	9
α-helix	738-753	16
α-helix	760	1
α-helix	762	1
α-helix	765-776	12
α-helix	781-806	26
β-strand	819-820	2	5
α-helix	821-824	4
β-strand	829-831	3	1
α-helix	939-965	27
α-helix	974-976	3
β-strand	985-990	6	14
β-strand	1001	1	15
β-strand	1007-1008	2	15
β-strand	1017	1	16
β-strand	1020-1021	2	15
α-helix	1022-1025	4
β-strand	1038	1	16
β-strand	1047-1049	3	17
β-strand	1057-1060	4	17
β-strand	1065-1069	5	17
β-strand	1084-1089	6	17
β-strand	1098-1105	8	18
β-strand	1110-1116	7	18
β-strand	1121	1	19
β-strand	1122-1125	4	18
β-strand	1131	1	18
β-strand	1135	1	19
β-strand	1144-1149	6	20
β-strand	1155-1160	6	20
β-strand	1166-1169	4	20
β-strand	1174-1178	5	20
β-strand	1187-1192	6	21
β-strand	1199-1204	6	21
β-strand	1210-1214	5	21
β-strand	1219-1226	8	21
α-helix	1230	1
β-strand	1242-1247	6	22
β-strand	1256-1260	5	22
β-strand	1266-1268	3	22
α-helix	1273-1275	3
β-strand	1277-1278	2	22
β-strand	1289-1292	4	21
α-helix	1295-1297	3
β-strand	1300-1304	5	21
β-strand	1332-1339	8	14
β-strand	1343-1349	7	14
β-strand	1353-1357	5	14

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
β-strand	18-26	9	2
α-helix	35-40	6
α-helix	42-45	4
α-helix	48-51	4
β-strand	58-64	7	3
β-strand	74-75	2	3
α-helix	76-78	3
β-strand	85-96	12	2
β-strand	105-113	9	3
β-strand	119-128	10	3
β-strand	130	1	4
β-strand	135	1	1
β-strand	136	1	4
β-strand	139-140	2	2
β-strand	143-144	2	2
β-strand	146-147	2	3
β-strand	160	1	3
α-helix	171-183	13
α-helix	191-211	21
β-strand	216-217	2	2
β-strand	220-221	2	2
β-strand	224-226	3	5
β-strand	229-231	3	5
β-strand	232-234	3	1
α-helix	265-273	9

Chain C: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	76-97	22
α-helix	102-204	103
β-strand	208-210	3	6
β-strand	260-263	4	6
β-strand	269-271	3	6
α-helix	276-278	3
α-helix	299-321	23
α-helix	331-335	5
α-helix	338-340	3
α-helix	341-361	21
α-helix	374-382	9

Chain D: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	138-266	129
α-helix	269-273	5
β-strand	276-277	2	7
β-strand	283-285	3	7
β-strand	288-290	3	7
α-helix	300-321	22
β-strand	328-331	4	8
β-strand	338-341	4	8
β-strand	350	1	8
α-helix	364-384	21
β-strand	396-397	2	9
β-strand	402-403	2	9
β-strand	414	1	9
α-helix	422-447	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	Q6ZNE5 (AlphaFold model)
Beclin-1	D	protein	450	Homo sapiens	Q14457 (AlphaFold model)
Phosphoinositide 3-kinase regulatory subunit 4	A	protein	1358	Homo sapiens	Q99570 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>13BV_1 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 2 (C), FASTA

>13BV_2 Beclin 1-associated autophagy-related key regulator (chains C)
MASPSGKGARALEAPGCGPRPLARDLVDSVDDAEGLYVAVERCPLCNTTRRRLTCAKCVQ
SGDFVYFDGRDRERFIDKKERLSRLKSKQEEFQKEVLKAMEGKWITDQLRWKIMSCKMRI
EQLKQTICKGNEEMEKNSEGLLKTKEKNQKLYSRAQRHQEKKEKIQRHNRKLGDLVEKKT
IDLRSHYERLANLRRSHILELTSVIFPIEEVKTGVRDPADVSSESDSAMTSSTVSKLAEA
RRTTYLSGRWVCDDHNGDTSISITGPWISLPNNGDYSAYYSWVEEKKTTQGPDMEQSNPA
YTISAALCYATQLVNILSHILDVNLPKKLCNSEFCGENLSKQKFTRAVKKLNANILYLCF
SQHVNLDQLQPLHTLRNLMYLVSPSSEHLGRSGPFEVRADLEESMEFVDPGVAGESDESG
DERVSDEETDLGTDWENLPSPRFCDIPSQSVEVSQSQSTQASPPIASSSAGGMISSAAAS
VTSWFKAYTGHR

Sequence of entity 3 (D), FASTA

>13BV_3 Beclin-1 (chains D)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Sequence of entity 4 (A), FASTA

>13BV_4 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

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MYR	Myristic acid	C14 H28 O2	1

Primary citation

Cryo-EM reconstruction of PI3KC3-C2 in complex with Rubicon Middle Region of C terminus. Chen, M., Hurley, J.H. To be published.

Other PDB entries of the same protein (UniProt Q8NEB9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HOG 1.26 Å, Structure of VPS34 LIR motif bound to GABARAP
7RSP 1.67 Å, Structure of the VPS34 kinase domain with compound 14
7RSV 1.78 Å, Structure of the VPS34 kinase domain with compound 5
7RSJ 1.88 Å, Structure of the VPS34 kinase domain with compound 14
4UWH 1.93 Å, Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo-…
9NIN 2.01 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-86
8RXR 2.06 Å, Crystal structure of VPS34 in complex with inhibitor SB02024
9ORM 2.06 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-I-137
6I3U 2.09 Å, Optimization of potent and selective ATM inhibitors suitable for a proof-of-concept…
9ZF4 2.09 Å, The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83
9DKP 2.16 Å, The structure of human vacuolar protein sorting 34 catalytic domain bound to RD-I-53
3LS8 2.25 Å, Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimi…

Browse structure collections

About this viewer

MolViewer shows 13BV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.