9RXA: VPS34-CII

VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit. Determined by electron microscopy at 4.0 Å resolution. Released 3 Jun 2026.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 24,055
Mol. weight: 411.22 kDa
Ligands: ZN, MYR, MG, GDP
Released: 3 Jun 2026

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

Secondary structure: helices and β-sheets

9RXA contains 148 α-helices and 121 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, 28 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	18-27	10	2
α-helix	30-34	5
α-helix	35-40	6
α-helix	42-46	5
β-strand	58-65	8	3
β-strand	68-69	2	3
β-strand	74-75	2	3
β-strand	86-96	11	2
β-strand	105-115	11	3
β-strand	118-128	11	3
β-strand	130	1	4
β-strand	135	1	5
β-strand	136	1	4
α-helix	137	1
β-strand	140-145	6	2
β-strand	146-147	2	3
α-helix	173-183	11
α-helix	191-211	21
β-strand	215-220	6	2
β-strand	223-225	3	6
β-strand	230-231	2	6
β-strand	232-233	2	1
β-strand	234	1	5
α-helix	265-274	10
α-helix	281-285	5
α-helix	286-289	4
α-helix	290-300	11
α-helix	306-308	3
α-helix	310-318	9
α-helix	322-325	4
α-helix	330-334	5
α-helix	342-350	9
α-helix	351-353	3
α-helix	356-357	2
α-helix	362-365	4
α-helix	374-384	11
α-helix	388	1
α-helix	392-395	4
α-helix	396-401	6
α-helix	402-405	4
α-helix	408-411	4
α-helix	475-483	9
α-helix	487-500	14
α-helix	504-509	6
α-helix	511-529	19
α-helix	533-561	29
α-helix	566-577	12
β-strand	591-592	2	7
β-strand	600-604	5	7
β-strand	610-611	2	7
β-strand	619-625	7	7
β-strand	630-637	8	7
α-helix	641-660	20
β-strand	672-674	3	7
β-strand	679-683	5	7
β-strand	688-689	2	8
α-helix	690-696	7
α-helix	700-707	8
α-helix	719-739	21
β-strand	749-751	3	8
β-strand	757-759	3	8
α-helix	774-775	2
α-helix	781-786	6
α-helix	793-809	17
α-helix	813-822	10
α-helix	823-825	3
α-helix	829-832	4
α-helix	838-846	9
α-helix	852-868	17

Chain B: 62 helices, 58 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	27-34	8	9
β-strand	39-44	6	9
β-strand	49-56	8	9
α-helix	65-77	13
β-strand	84	1	10
β-strand	89-95	7	9
β-strand	98-104	7	9
β-strand	108-109	2	10
α-helix	110-113	4
α-helix	119-120	2
α-helix	122-140	19
α-helix	151-153	3
β-strand	154-156	3	10
β-strand	162-164	3	10
β-strand	175-176	2	11
α-helix	183-186	4
β-strand	194	1	12
α-helix	199-201	3
β-strand	202-203	2	11
α-helix	237-252	16
β-strand	260	1	12
α-helix	261-269	9
α-helix	278-280	3
α-helix	284-293	10
α-helix	304-310	7
β-strand	312	1	13
β-strand	316	1	13
α-helix	320-324	5
α-helix	325-327	3
α-helix	339-348	10
α-helix	350-358	9
α-helix	375-384	10
α-helix	392-405	14
α-helix	411-417	7
α-helix	419-424	6
α-helix	425-427	3
α-helix	431-445	15
α-helix	451-452	2
α-helix	459-463	5
α-helix	468-472	5
α-helix	476-483	8
α-helix	486-505	20
α-helix	523-544	22
α-helix	550-558	9
α-helix	562-568	7
α-helix	570-572	3
α-helix	573-577	5
α-helix	583-586	4
α-helix	592-599	8
α-helix	601-608	8
α-helix	610-612	3
α-helix	613-623	11
α-helix	629-645	17
α-helix	652-660	9
α-helix	661-665	5
α-helix	669-685	17
α-helix	688-690	3
α-helix	691-695	5
α-helix	696-698	3
β-strand	703	1	14
α-helix	717-719	3
β-strand	720	1	14
α-helix	722-725	4
α-helix	726-732	7
α-helix	738-753	16
α-helix	759-762	4
α-helix	765-776	12
α-helix	781-789	9
α-helix	791-808	18
α-helix	809-812	4
β-strand	818-820	3	6
α-helix	821-824	4
α-helix	827-828	2
β-strand	829-832	4	1
α-helix	940-965	26
α-helix	974-976	3
β-strand	985	1	15
β-strand	990	1	16
β-strand	999-1001	3	17
β-strand	1007	1	18
β-strand	1008-1011	4	17
β-strand	1017-1019	3	17
β-strand	1021	1	18
α-helix	1022-1024	3
β-strand	1036-1038	3	17
β-strand	1045-1050	6	19
β-strand	1057-1061	5	19
β-strand	1065-1068	4	19
β-strand	1072	1	20
β-strand	1081	1	20
β-strand	1088-1089	2	19
β-strand	1097-1103	7	21
β-strand	1111-1116	6	21
β-strand	1120-1125	6	21
β-strand	1131-1136	6	21
α-helix	1139-1141	3
β-strand	1144-1146	3	22
β-strand	1149	1	22
β-strand	1155-1160	6	22
β-strand	1164-1169	6	22
β-strand	1175-1180	6	22
β-strand	1187	1	23
β-strand	1191-1192	2	24
β-strand	1199-1203	5	24
β-strand	1204	1	23
β-strand	1210-1214	5	24
β-strand	1219-1225	7	24
α-helix	1230	1
β-strand	1242-1247	6	25
β-strand	1256-1260	5	25
β-strand	1264-1268	5	25
α-helix	1273-1275	3
β-strand	1279-1281	3	25
β-strand	1290-1295	6	24
β-strand	1298-1303	6	24
β-strand	1332-1339	8	15
β-strand	1343-1349	7	15
β-strand	1354	1	16
β-strand	1355-1357	3	15

Chain C: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	26
β-strand	24-25	2	26
α-helix	29-32	4
α-helix	36-42	7
α-helix	111-127	17
α-helix	138-169	32
α-helix	177-264	88
β-strand	276-279	4	27
β-strand	282-285	4	27
β-strand	288	1	27
α-helix	300-302	3
α-helix	307-310	4
α-helix	311-314	4
α-helix	315-321	7
β-strand	328-331	4	28
α-helix	334-336	3
β-strand	338-341	4	28
β-strand	348-350	3	28
α-helix	356-361	6
α-helix	364-366	3
α-helix	367-370	4
α-helix	371-375	5
α-helix	376-380	5
β-strand	394-397	4	29
β-strand	402-405	4	29
α-helix	422-425	4
α-helix	426-428	3
α-helix	430-438	9
α-helix	447-449	3

Chain D: 17 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	47-50	4	30
α-helix	58-60	3
β-strand	63-69	7	31
β-strand	82	1	31
β-strand	86-87	2	31
β-strand	93	1	30
β-strand	112-121	10	31
β-strand	124-134	11	31
α-helix	135-137	3
α-helix	138	1
β-strand	139-142	4	30
α-helix	152	1
β-strand	153-156	4	30
β-strand	161-163	3	30
β-strand	188	1	26
α-helix	193-225	33
α-helix	228-288	61
α-helix	290-323	34
α-helix	324-327	4
β-strand	331-332	2	32
β-strand	340-341	2	32
β-strand	344-345	2	32
α-helix	360-363	4
α-helix	365-377	13
α-helix	380-382	3
β-strand	386	1	33
α-helix	390-392	3
β-strand	394-396	3	33
α-helix	401-403	3
β-strand	409-411	3	33
α-helix	424-432	9
α-helix	435-439	5
α-helix	452-455	4

Chain F: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-26	9	34
α-helix	33-41	9
α-helix	49-51	3
β-strand	56-63	8	34
β-strand	68-75	8	34
α-helix	80-85	6
α-helix	86-89	4
β-strand	95-101	7	34
α-helix	105-121	17
β-strand	127-133	7	34
α-helix	135-140	6
α-helix	145-154	10
β-strand	158-161	4	34
β-strand	163	1	35
β-strand	168	1	35
α-helix	172-180	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 3-kinase catalytic subunit type 3	A	protein	887	Homo sapiens	Q8NEB9 (AlphaFold model)
Phosphoinositide 3-kinase regulatory subunit 4	B	protein	1370	Homo sapiens	Q99570 (AlphaFold model)
Beclin-1	C	protein	450	Homo sapiens	Q14457 (AlphaFold model)
UV radiation resistance associated protein	D	protein	699	Homo sapiens	Q6P1X0 (AlphaFold model)
Ras-related protein Rab-5A	F	protein	212	Homo sapiens	P20339

Sequence of entity 1 (A), FASTA

>9RXA_1 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains A)
MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLYVT
CQVFAEGKPLALPVRTSYKAFSTRWNWNEWLKLPVKYPDLPRNAQVALTIWDVYGPGKAV
PVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTPGRTSSTLSEDQMSRLAKLTK
AHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYGIVYYEKDG
DESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNAATRDQLNIIV
SYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDV
EDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKK
DSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLI
SRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRS
LLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVK
IRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRK
ENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAE
VMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLN
KEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVK
KVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIHKFAQYWRK

Sequence of entity 2 (B), FASTA

>9RXA_2 Phosphoinositide 3-kinase regulatory subunit 4 (chains B)
GNQLAGIAPSQILSVESYFSDIHDFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDPT
LPLTSYKQELEELKIRLNSAQNCLPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFLN
NIEKRWIAFQILTAVDQAHKSGVRHGDIKTENVMVTSWNWVLLTDFASFKPTYLPEDNPA
DFNYFFDTSRRRTCYIAPERFVDGGMFATELEYMRDPSTPLVDLNSNQRTRGELKRAMDI
FSAGCVIAELFTEGVPLFDLSQLLAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDKR
LEAEDYLKQQRGNAFPEIFYTFLQPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGHD
LPEKAEGEPKENGLVILVSVITSCLQTLKYCDSKLAALELILHLAPRLSVEILLDRITPY
LLHFSNDSVPRVRAEALRTLTKVLALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRLA
YAENIALLAETALRFLELVQLKNLNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQKV
VTLLSDPENIVKQTLMENGITRLCVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDSI
VGVAAYVGWQSSSILKPLLQQGLSDAEEFVIVKALYALTCMCQLGLLQKPHVYEFASDIA
PFLCHPNLWIRYGAVGFITVVARQISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVLK
EPVSRSIFDYALRSKDITSLFRHLHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMTE
EEEDKLLALKDFMMKSNKAKANIVDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEPD
DKRARKHVKQDSNVNEEWKSMFGSLDPPNMPQALPKGSDQEVIQTGKPPRSESSAGICVP
LSTSSQVPEVTTVQNKKPVIPVLSSTILPSTYQIRITTCKTELQQLIQQKREQCNAERIA
KQMMENAEWESKPPPPGWRPKGLLVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIWN
SQKMEGKTTTTRSILTYSRIGGRVKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSPK
IHPLQSRILDQKEDGCVVDMHHFNSGAQSVLAYATVNGSLVGWDLRSSSNAWTLKHDLKS
GLITSFAVDIHQCWLCIGTSSGTMACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWVI
AAVQGNNEVSMWDMETGDRRFTLWASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAGS
DMKIRFWDLAYPERSYVVAGSTSSPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRGP
ESLPVGHHDIITDVATFQTTQGFIVTASRDGIVKVWKSRPTTASENLYFQ

Sequence of entity 3 (C), FASTA

>9RXA_3 Beclin-1 (chains C)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Sequence of entity 4 (D), FASTA

>9RXA_4 UV radiation resistance associated protein (chains D)
MSASASVGGQVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQ
LLDTYFTLHLCSTEKIYKEFYRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGG
KENIYQLLIEWKVCLDGLKYLGQQIHARNQNEIIFGLNDGYYGAPFEHKGYSNAQKTILL
QVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECL
QLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKEC
TAKRELFLKTNAQLTIRCRQLLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSI
AVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNINDKLTEKEREFPLYPKGGEKL
QFDYGVYLLNKNIAQLRYQHGLGTPDLRQTLPNLKNFMEHGLMVRCDRHHTSSAIPVPKR
QSSIFGGADVGFSGGIPSPDKGHRKRASSENERLQYKTPPPSYNSALAQPVTTVPSMGET
ERKITSLSSSLDTSLDFSKENKKKGEDLVGSLNGGHANVHPSQEQGEALSGHRATVNGTL
LPSEQAGSASVQLPGEFHPVSEAELCCTVEQAEEIIGLEATGFASGDQLEAFNCIPVDSA
VAVECDEQVLGEFEEFSRRIYALNENVSSFRRPRRSSDK

Sequence of entity 5 (F), FASTA

>9RXA_5 Ras-related protein Rab-5A (chains F)
MASRGATRPNGPNTGNKISQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQ
TVSLDDTTVKFEIWDTAGLERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQR
QASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKK
LPKNEPQNPGANSARGRGVDLTEPTQPTRNQC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MYR	Myristic acid	C14 H28 O2	1
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

A novel RAB5 binding site in human VPS34-CII that is likely the primordial site in eukaryotic evolution. Spokaite, S., Ohashi, Y., Bourguet, M. et al. Elife (2026) 15. DOI 10.7554/eLife.110040 · PubMed

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…

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