9ZPC: Human PI3KC3-C2

Cryo-EM structure of human PI3KC3-C2. Determined by electron microscopy at 3.83 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 3.83 Å
Organism: Homo sapiens
Chains: 4
Atoms: 16,275
Mol. weight: 395.26 kDa
Ligands: GDP, MG, ZN
Released: 24 Dec 2025

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

Secondary structure: helices and β-sheets

9ZPC contains 86 α-helices and 83 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: 55 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	41-44	4	1
β-strand	49-53	5	1
α-helix	67-78	12
β-strand	84-85	2	2
β-strand	101-104	4	1
α-helix	105-106	2
α-helix	111-115	5
α-helix	122-141	20
β-strand	154-156	3	2
β-strand	162-165	4	2
α-helix	181-182	2
α-helix	183-187	5
α-helix	237-252	16
α-helix	261-268	8
α-helix	275-278	4
α-helix	284-293	10
α-helix	298-300	3
α-helix	304-310	7
α-helix	318-319	2
α-helix	320-324	5
α-helix	325-330	6
α-helix	339-356	18
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	419-426	8
α-helix	431-446	16
α-helix	453-455	3
α-helix	458	1
α-helix	459-463	5
α-helix	464-472	9
α-helix	476-500	25
α-helix	526-546	21
α-helix	550-559	10
α-helix	561-568	8
α-helix	570-572	3
α-helix	573-577	5
α-helix	578-584	7
α-helix	591-607	17
α-helix	609-611	3
α-helix	613-624	12
α-helix	629-644	16
α-helix	650-660	11
α-helix	662-665	4
α-helix	670-685	16
α-helix	688-690	3
α-helix	691-695	5
α-helix	696-699	4
β-strand	703	1	3
α-helix	713-719	7
β-strand	720	1	3
α-helix	721-725	5
α-helix	726-734	9
α-helix	738-753	16
α-helix	765-776	12
α-helix	781-789	9
α-helix	791-802	12
β-strand	985-989	5	4
β-strand	996-1002	7	5
β-strand	1007-1012	6	5
β-strand	1018-1021	4	5
β-strand	1036	1	5
β-strand	1048-1050	3	6
β-strand	1056-1060	5	6
β-strand	1066-1072	7	6
β-strand	1081-1083	3	6
β-strand	1101-1104	4	7
β-strand	1111-1114	4	7
β-strand	1121-1125	5	7
β-strand	1130-1135	6	7
α-helix	1139-1141	3
β-strand	1144-1149	6	8
β-strand	1155-1160	6	8
β-strand	1165-1169	5	8
β-strand	1174-1176	3	8
β-strand	1187-1192	6	9
β-strand	1199-1204	6	9
β-strand	1209-1214	6	9
β-strand	1219-1225	7	9
α-helix	1230	1
β-strand	1242-1250	9	10
β-strand	1253-1260	8	10
β-strand	1265-1269	5	10
α-helix	1273-1275	3
β-strand	1277-1278	2	10
α-helix	1286-1287	2
β-strand	1288-1295	8	9
β-strand	1298-1305	8	9
β-strand	1332-1339	8	4
β-strand	1343-1349	7	4
β-strand	1354-1357	4	4

Chain B: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	11
β-strand	18-28	11	12
α-helix	35-40	6
α-helix	42-46	5
α-helix	54-55	2
β-strand	58-65	8	13
β-strand	68-69	2	13
α-helix	72-73	2
β-strand	74	1	13
α-helix	76-78	3
β-strand	85	1	12
β-strand	89-96	8	12
α-helix	97-99	3
β-strand	105-115	11	13
β-strand	118-128	11	13
β-strand	130	1	14
α-helix	132-134	3
β-strand	135	1	11
β-strand	136	1	14
β-strand	141-145	5	12
β-strand	146	1	13
β-strand	160	1	13
α-helix	172-183	12
α-helix	191-211	21
β-strand	215-221	7	12
β-strand	232-234	3	11
α-helix	265-271	7

Chain C: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	45-51	7	15
α-helix	53-55	3
β-strand	64-69	6	16
α-helix	77-79	3
β-strand	86	1	16
β-strand	112-119	8	16
β-strand	127	1	16
β-strand	131-134	4	16
α-helix	135-137	3
β-strand	139-141	3	15
β-strand	152-157	6	15
β-strand	160-163	4	15
β-strand	189	1	17
β-strand	190	1	18
α-helix	191-192	2
α-helix	193-328	136
β-strand	332-333	2	19
α-helix	338	1
β-strand	339-341	3	19
β-strand	344-346	3	19
α-helix	360-378	19
β-strand	386-387	2	20
β-strand	394-396	3	20
α-helix	406-408	3
β-strand	409-411	3	20
α-helix	419-440	22
α-helix	451-460	10

Chain D: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	21
β-strand	24	1	21
β-strand	26	1	17
α-helix	27-28	2
α-helix	29-33	5
α-helix	36-42	7
β-strand	81-82	2	16
α-helix	111-129	19
β-strand	137	1	18
α-helix	138-170	33
α-helix	177-266	90
α-helix	269-273	5
β-strand	277-279	3	22
β-strand	282-284	3	22
β-strand	285	1	23
β-strand	288	1	23
α-helix	300-321	22
α-helix	367-386	20
β-strand	396-397	2	24
β-strand	402-403	2	24
α-helix	425-446	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphoinositide 3-kinase regulatory subunit 4	A	protein	1445	Homo sapiens	A0JP11
Phosphatidylinositol 3-kinase catalytic subunit type 3	B	protein	887	Homo sapiens	Q8NEB9 (AlphaFold model)
UV radiation resistance-associated gene protein	C	protein	699	Homo sapiens	Q9P2Y5 (AlphaFold model)
Beclin-1	D	protein	450	Homo sapiens	Q14457 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9ZPC_1 Phosphoinositide 3-kinase regulatory subunit 4 (chains A)
MFMPSSFSYSSWATCWLLCCLIILAKNSSIDGIEATMGNQLAGIAPSQILSVESYFSDIH
DFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDPTLPLTSYKQELEELKIRLNSAQNC
LPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFLNNIEKRWIAFQILTAVDQAHKSGV
RHGDIKTENVMVTSWNWVLLTDFASFKPTYLPEDNPADFNYFFDTSRRRTCYIAPERFVD
GGMFATELEYMRDPSTPLVDLNSNQRRRGELKRAMDIFSAGCVIAELFTEGVPLFDLSQL
LAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDKRLEAEDYLKQQRGNAFPEIFYTFL
QPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGHDLPEKAEGEPKENGLVILVSVITS
CLQTLKYCDSKLAALELILHLAPRLSVEILLDRITPYLLHFSNDSVPRVRAEALRTLTKV
LALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRLAYAENIALLAETALRFLELVQLKN
LNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQKVVTLLSDPENIVKQTLMENGITRL
CVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDSIVGVAAYVGWQSSSILKPLLQQGL
SDAEEFVIVKALYALTCMCQLGLLQKPHVYEFASDIAPFLCHPNLWIRYGAVGFITVVAR
QISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVLKEPVSRSIFDYALRSKDITSLFRH
LHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMTEEEEDKLLALKDFMMKSNKAKANI
VDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEPDDKRARKHVKQDSNVNEEWKSMFG
SLDPPNMPQALPKGSDQEVIQTGKPPRSESSAGICVPLSTSSQVPEVTTVQNKKPVIPVL
SSTILPSTYQIRITTCKTELQQLIQQKREQCNAERIAKQMMENAEWESKPPPPGWRPKGL
LVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIWNSQKMEGKTTTTRSILTYSRIGGR
VKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSPKIHPLQSRILDQKEDGCVVDMHHF
NSGAQSVLAYATVNGSLVGWDLRSSSNAWTLKHDLKSGLITSFAVDIHQCWLCIGTSSGT
MACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWVIAAVQGNNEVSMWDMETGDRRFTL
WASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAGSDMKIRFWDLAYPERSYVVAGSTS
SPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRGPESLPVGHHDIITDVATFQTTQGF
IVTASRDGIVKVWKGTENLYFQSGMAAWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYK
DDDDK

Sequence of entity 2 (B), FASTA

>9ZPC_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

>9ZPC_3 UV radiation resistance-associated gene protein (chains C)
MSASASVGGPVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQ
LLDTYFTLHLCSTEKIYKEFYRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGG
KENIYQLLIEWKVCLDGLKYLGQQIHARNQNEIIFGLNDGYYGAPFEHKGYSNAQKTILL
QVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECL
QLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKEC
TAKRELFLKTNAQLTIRCRQLLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSI
AVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNINDKLTEKEREFPLYPKGGEKL
QFDYGVYLLNKNIAQLRYQHGLGTPDLRQTLPNLKNFMEHGLMVRCDRHHTSSAIPVPKR
QSSIFGGADVGFSGGIPSPDKGHRKRASSENERLQYKTPPPSYNSALAQPVTTVPSMGET
ERKITSLSSSLDTSLDFSKENKKKGEDLVGSLNGGHANVHPSQEQGEALSGHRATVNGTL
LPSEQAGSASVQLPGEFHPVSEAELCCTVEQAEEIIGLEATGFASGDQLEAFNCIPVDSA
VAVECDEQVLGEFEEFSRRIYALNENVSSFRRPRRSSDK

Sequence of entity 4 (D), FASTA

>9ZPC_4 Beclin-1 (chains D)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1

Primary citation

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

Other PDB entries of the same protein (UniProt A0JP11), best resolution first:

9ZPD 3.38 Å, Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus

Browse structure collections

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