9RX5: VPS34-CII

VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L). Determined by electron microscopy at 3.15 Å resolution. Released 3 Jun 2026.

Method: Electron microscopy
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 6
Atoms: 25,422
Mol. weight: 434.86 kDa
Ligands: MYR, GDP, MG, ZN
Released: 3 Jun 2026

Explore 9RX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RX5 contains 151 α-helices and 129 β-strands across 6 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: 44 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	18-27	10	2
α-helix	30-33	4
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
α-helix	76-78	3
β-strand	86-96	11	2
α-helix	97-99	3
β-strand	104-115	12	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	191-210	20
β-strand	215-220	6	2
β-strand	223-225	3	6
β-strand	230	1	6
β-strand	232-233	2	1
β-strand	234	1	5
α-helix	243-246	4
α-helix	265-274	10
α-helix	281-285	5
α-helix	290-300	11
α-helix	306-308	3
α-helix	310-318	9
α-helix	322-325	4
α-helix	327-329	3
α-helix	330-333	4
α-helix	342-352	11
α-helix	356-359	4
α-helix	362-364	3
α-helix	374-384	11
α-helix	388	1
α-helix	393-395	3
α-helix	396-402	7
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
α-helix	588-590	3
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	642-659	18
β-strand	672-674	3	7
β-strand	679-683	5	7
β-strand	688-689	2	8
α-helix	690-697	8
α-helix	700-707	8
β-strand	709	1	9
β-strand	717	1	9
α-helix	719-739	21
β-strand	749-751	3	8
β-strand	757-759	3	8
α-helix	781-786	6
α-helix	793-809	17
α-helix	813-820	8
α-helix	821-823	3
α-helix	829-833	5
α-helix	835-837	3
α-helix	838-846	9
α-helix	852-868	17

Chain B: 63 helices, 53 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	19-21	3
β-strand	27-34	8	10
β-strand	39-44	6	10
β-strand	49-56	8	10
α-helix	65-77	13
β-strand	84	1	11
β-strand	89-91	3	10
β-strand	98-104	7	10
β-strand	108-109	2	11
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	11
β-strand	162-164	3	11
β-strand	175-176	2	12
α-helix	183-186	4
β-strand	194	1	13
α-helix	199-201	3
β-strand	202-203	2	12
α-helix	238-252	15
β-strand	260	1	13
α-helix	261-269	9
α-helix	278-280	3
α-helix	284-293	10
α-helix	304-310	7
β-strand	312	1	14
β-strand	316	1	14
α-helix	320-324	5
α-helix	325-328	4
α-helix	339-357	19
α-helix	375-384	10
α-helix	392-405	14
α-helix	406-408	3
α-helix	411-413	3
α-helix	414-418	5
α-helix	419-424	6
α-helix	425-427	3
α-helix	431-444	14
α-helix	445-447	3
α-helix	451-452	2
α-helix	459-463	5
α-helix	464-467	4
α-helix	468-472	5
α-helix	476-482	7
α-helix	486-505	20
α-helix	523-545	23
α-helix	550-558	9
α-helix	561-568	8
α-helix	570-572	3
α-helix	573-577	5
α-helix	583-586	4
α-helix	591-608	18
α-helix	610-614	5
α-helix	617-623	7
α-helix	629-644	16
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	696-699	4
β-strand	703	1	15
α-helix	717-719	3
β-strand	720	1	15
α-helix	721-725	5
α-helix	726-734	9
α-helix	738-753	16
α-helix	759-762	4
α-helix	765-777	13
α-helix	782-788	7
α-helix	791-808	18
α-helix	809-812	4
β-strand	818-820	3	6
α-helix	821-824	4
α-helix	826-828	3
β-strand	829-832	4	1
α-helix	940-965	26
α-helix	974-976	3
β-strand	985	1	16
β-strand	998-1001	4	17
β-strand	1007-1011	5	17
β-strand	1017-1021	5	17
β-strand	1036-1038	3	17
β-strand	1045-1050	6	18
β-strand	1057-1061	5	18
β-strand	1065-1068	4	18
β-strand	1072	1	19
β-strand	1081	1	19
β-strand	1088-1089	2	18
β-strand	1100-1103	4	20
β-strand	1111-1115	5	20
β-strand	1120-1125	6	20
β-strand	1131-1136	6	20
β-strand	1144-1149	6	21
β-strand	1155-1160	6	21
β-strand	1164	1	22
β-strand	1165-1169	5	21
β-strand	1174-1175	2	21
β-strand	1180	1	22
β-strand	1187-1192	6	23
β-strand	1199-1204	6	23
β-strand	1210-1214	5	23
β-strand	1222-1225	4	23
α-helix	1230	1
β-strand	1242-1247	6	24
β-strand	1255-1260	6	24
β-strand	1265-1269	5	24
α-helix	1273-1275	3
β-strand	1280	1	24
β-strand	1290-1295	6	23
β-strand	1298-1303	6	23
β-strand	1332-1339	8	16
β-strand	1343-1349	7	16
β-strand	1355-1357	3	16

Chain C: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	25
β-strand	24-25	2	25
α-helix	30-33	4
α-helix	36-42	7
α-helix	111-127	17
α-helix	139-168	30
α-helix	169-171	3
α-helix	177-266	90
α-helix	269-273	5
β-strand	276-279	4	26
β-strand	282-285	4	26
β-strand	288-289	2	26
α-helix	300-321	22
β-strand	328-331	4	27
α-helix	334-336	3
β-strand	338-341	4	27
β-strand	349-350	2	27
α-helix	356-360	5
α-helix	363-383	21
β-strand	394-397	4	28
β-strand	402-405	4	28
β-strand	413-414	2	28
α-helix	422-443	22
α-helix	447-449	3

Chain D: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	47-50	4	29
α-helix	58-60	3
β-strand	63-69	7	30
β-strand	81-82	2	30
β-strand	86	1	30
β-strand	93	1	29
α-helix	95-97	3
β-strand	112-121	10	30
β-strand	124-134	11	30
α-helix	135-137	3
β-strand	139-142	4	29
β-strand	153-157	5	29
β-strand	160-163	4	29
β-strand	188	1	25
α-helix	193-225	33
α-helix	228-289	62
α-helix	292-324	33
α-helix	325-327	3
β-strand	331-333	3	31
β-strand	339-341	3	31
β-strand	344-345	2	31
α-helix	349-352	4
α-helix	360-377	18
β-strand	386-387	2	32
α-helix	390-392	3
β-strand	394-396	3	32
α-helix	406-408	3
β-strand	409-411	3	32
α-helix	420-438	19
α-helix	451-458	8

Chain E: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18-27	10	33
α-helix	33-41	9
α-helix	50-52	3
β-strand	56-58	3	33
β-strand	62-63	2	33
β-strand	68-75	8	33
α-helix	80-82	3
α-helix	87-90	4
β-strand	95-101	7	33
α-helix	105-117	13
α-helix	118-122	5
β-strand	127-133	7	33
α-helix	135-140	6
α-helix	145-154	10
β-strand	158-161	4	33
β-strand	163	1	34
β-strand	168	1	34
α-helix	170-180	11

Chain F: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18-27	10	35
α-helix	33-41	9
α-helix	50-52	3
β-strand	56-58	3	35
β-strand	62-64	3	35
β-strand	67-75	9	35
α-helix	86-89	4
β-strand	95-101	7	35
α-helix	105-117	13
α-helix	118-122	5
β-strand	127-133	7	35
α-helix	135-140	6
α-helix	145-155	11
β-strand	158-161	4	35
β-strand	163	1	36
β-strand	168	1	36
α-helix	170-180	11

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	E, F	protein	212	Homo sapiens	P20339

Sequence of entity 1 (A), FASTA

>9RX5_1 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains A)
MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLYVT
CQVFAEGKPLALPVRTSYKAFSTRWNWNEWLKLPVKYPDLPRNAQVALTIWDVYGPGKAV
PVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTPGRTSSTLSEDQMSRLAKLTK
AHRQGHMVKVDWLDRLTFAAAAMINESEKRSSNFMYLMVEFRCVKCDDKEYGIVYYEKDG
DESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNAATRDQLNIIV
SYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDV
EDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKK
DSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLI
SRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRS
LLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVK
IRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRK
ENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAE
VMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLN
KEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVK
KVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIHKFAQYWRK

Sequence of entity 2 (B), FASTA

>9RX5_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

>9RX5_3 Beclin-1 (chains C)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Sequence of entity 4 (D), FASTA

>9RX5_4 UV radiation resistance associated protein (chains D)
MSASASVGGQVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQ
LLDTYFTLHLCSTEKIYKEFYRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGG
KENIYQLLIEWKVCLDGLKYLGQQIHARNQNEIIFGLNDGYYGAPFEHKGYSNAQKTILL
QVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECL
QLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKEC
TAKRELFLKTNAQLTIRCRQLLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSI
AVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNINDKLTEKEREFPLYPKGGEKL
QFDYGVYLLNKNIAQLRYQHGLGTPDLRQTLPNLKNFMEHGLMVRCDRHHTSSAIPVPKR
QSSIFGGADVGFSGGIPSPDKGHRKRASSENERLQYKTPPPSYNSALAQPVTTVPSMGET
ERKITSLSSSLDTSLDFSKENKKKGEDLVGSLNGGHANVHPSQEQGEALSGHRATVNGTL
LPSEQAGSASVQLPGEFHPVSEAELCCTVEQAEEIIGLEATGFASGDQLEAFNCIPVDSA
VAVECDEQVLGEFEEFSRRIYALNENVSSFRRPRRSSDK

Sequence of entity 5 (E, F), FASTA

>9RX5_5 Ras-related protein Rab-5A (chains E, F)
MASRGATRPNGPNTGNKISQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQ
TVSLDDTTVKFEIWDTAGLERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQR
QASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKK
LPKNEPQNPGANSARGRGVDLTEPTQPTRNQC

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	3
ZN	Zinc ion	Zn	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

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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