9ZPD: Human PI3KC3-C2

Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus. Determined by electron microscopy at 3.38 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 3.38 Å
Organism: Homo sapiens
Chains: 5
Atoms: 17,403
Mol. weight: 493.97 kDa
Ligands: GTP, ZN
Released: 24 Dec 2025

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

Secondary structure: helices and β-sheets

9ZPD contains 92 α-helices and 96 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: 61 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	41-45	5	1
β-strand	48-53	6	1
α-helix	67-80	14
β-strand	84-85	2	2
β-strand	101-104	4	1
α-helix	105-106	2
β-strand	108	1	2
α-helix	110-114	5
α-helix	122-142	21
α-helix	151-153	3
β-strand	154-156	3	2
β-strand	162-165	4	2
α-helix	181-182	2
α-helix	183-187	5
β-strand	194	1	3
α-helix	237-252	16
β-strand	260	1	3
α-helix	261-269	9
α-helix	275-280	6
α-helix	284-293	10
α-helix	298-300	3
α-helix	304-311	8
α-helix	318-319	2
α-helix	320-324	5
α-helix	325-327	3
α-helix	328-332	5
α-helix	334-336	3
α-helix	339-348	10
α-helix	350-356	7
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	431-445	15
α-helix	453-455	3
α-helix	459-463	5
α-helix	464-466	3
α-helix	468-471	4
α-helix	476-502	27
α-helix	526-545	20
α-helix	550-558	9
α-helix	564-566	3
α-helix	570-572	3
α-helix	573-577	5
α-helix	578-581	4
α-helix	582-586	5
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	700-702	3
β-strand	703	1	4
α-helix	713-717	5
β-strand	720	1	4
α-helix	726-734	9
α-helix	738-752	15
α-helix	760-762	3
α-helix	765-776	12
α-helix	781-789	9
α-helix	791-803	13
α-helix	941-967	27
β-strand	985	1	5
β-strand	990	1	6
β-strand	996-1002	7	7
β-strand	1007-1012	6	7
β-strand	1017-1021	5	7
β-strand	1036	1	7
β-strand	1048-1050	3	8
β-strand	1056-1060	5	8
β-strand	1065-1071	7	8
β-strand	1082-1084	3	8
β-strand	1088-1089	2	8
β-strand	1101-1104	4	9
β-strand	1111-1114	4	9
β-strand	1122-1125	4	9
β-strand	1130-1134	5	9
β-strand	1144-1149	6	10
β-strand	1156-1160	5	10
β-strand	1165-1169	5	10
β-strand	1174-1179	6	10
β-strand	1187	1	11
β-strand	1192	1	12
β-strand	1199-1201	3	12
β-strand	1204	1	11
β-strand	1212-1214	3	12
β-strand	1220-1223	4	12
α-helix	1230	1
β-strand	1242-1248	7	13
β-strand	1255-1260	6	13
β-strand	1265-1269	5	13
α-helix	1273-1275	3
β-strand	1277-1278	2	13
α-helix	1285-1287	3
β-strand	1288-1290	3	14
β-strand	1293-1294	2	12
β-strand	1299-1300	2	12
β-strand	1303-1305	3	14
β-strand	1332-1336	5	5
β-strand	1345-1349	5	5
β-strand	1353	1	6
β-strand	1354-1357	4	5

Chain B: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	15
β-strand	18-27	10	16
α-helix	35-40	6
α-helix	42-44	3
α-helix	54-55	2
β-strand	58-65	8	17
β-strand	68-69	2	17
β-strand	74	1	17
β-strand	86-96	11	16
α-helix	97-99	3
β-strand	105-115	11	17
β-strand	118-121	4	17
β-strand	125-128	4	17
β-strand	130	1	18
β-strand	135	1	15
β-strand	136	1	18
β-strand	140-145	6	16
α-helix	150-152	3
β-strand	160	1	17
α-helix	172-183	12
α-helix	192-211	20
β-strand	215-220	6	16
β-strand	232-234	3	15
α-helix	265-272	8

Chain C: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	45-51	7	19
β-strand	63-71	9	20
β-strand	76-79	4	20
α-helix	83-85	3
β-strand	86	1	20
β-strand	93	1	19
α-helix	94-96	3
β-strand	112-121	10	20
β-strand	124-134	11	20
α-helix	135-137	3
α-helix	138	1
β-strand	139-141	3	19
β-strand	152-157	6	19
β-strand	161-163	3	19
β-strand	188-189	2	21
β-strand	190	1	22
α-helix	191-192	2
α-helix	193-323	131
α-helix	324-326	3
β-strand	331-333	3	23
β-strand	339-341	3	23
β-strand	344-345	2	23
α-helix	350-352	3
α-helix	358-378	21
β-strand	386-387	2	24
β-strand	394-396	3	24
α-helix	406-408	3
β-strand	409-411	3	24
α-helix	419-439	21
α-helix	450-460	11

Chain D: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	25
β-strand	24	1	25
β-strand	25-26	2	21
α-helix	29-32	4
α-helix	36-42	7
β-strand	80-82	3	20
α-helix	111-129	19
β-strand	137	1	22
α-helix	138-171	34
α-helix	177-264	88
α-helix	269-273	5
β-strand	276-278	3	26
β-strand	283-285	3	26
β-strand	288-290	3	26
α-helix	300-321	22
β-strand	328-331	4	27
β-strand	338-341	4	27
β-strand	348-350	3	27
α-helix	363-386	24
β-strand	395-397	3	28
β-strand	402-404	3	28
β-strand	412-414	3	28
α-helix	422-446	25

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	489-514	26

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,Run domain Beclin-1-interacting and cysteine-rich domain-containing protein chimera	D, E	protein	663	Homo sapiens	Q14457 (AlphaFold model), Q92622

Sequence of entity 1 (A), FASTA

>9ZPD_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

>9ZPD_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

>9ZPD_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, E), FASTA

>9ZPD_4 Beclin-1,Run domain Beclin-1-interacting and cysteine-rich domain-containing protein chimera (chains D, E)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNKGGSGGSGGSGGSQSLISYLSEQDFGSCADL
EKENAHFSISESLIAAIELMKCNMMSQCLEEEEVEEEDSDREIQELKQKIRLRRQQIRTK
NLLPMYQEAEHGSFRVTSSSSQFSSRDSAQLSDSGSADEVDEFEIQDADIRRNTASSSKS
FVSSQSFSHCFLHSTSAEAVAMGLLKQFEGMQLPAASELEWLVPEHDAPQKLLPIPDSLP
ISP

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	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., Ni, Q., Hurley, J.H. To be published.

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

9ZPC 3.83 Å, Cryo-EM structure of human PI3KC3-C2

Browse structure collections

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