9RX4: VPS34-CI

VPS34-CI bound to NRBF2 and RAB1A. Determined by electron microscopy at 3.67 Å resolution. Released 22 Jul 2026.

Method: Electron microscopy
Resolution: 3.67 Å
Organism: Homo sapiens
Chains: 7
Atoms: 23,875
Mol. weight: 474.77 kDa
Ligands: MYR, MG, GDP, GTP
Released: 22 Jul 2026

Explore 9RX4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RX4 contains 152 α-helices and 104 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: 42 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	1
β-strand	18-27	10	2
α-helix	32-34	3
α-helix	35-40	6
α-helix	42-45	4
β-strand	47	1	3
β-strand	58-65	8	4
β-strand	68-69	2	4
β-strand	74-75	2	4
β-strand	86-96	11	2
α-helix	97-99	3
β-strand	105-113	9	4
β-strand	114	1	3
β-strand	119-128	10	4
β-strand	130	1	5
α-helix	135	1
β-strand	136	1	5
α-helix	137	1
β-strand	139-145	7	2
β-strand	146-147	2	4
α-helix	171-183	13
α-helix	191-207	17
α-helix	209-211	3
β-strand	215-221	7	2
β-strand	223-224	2	6
β-strand	225-226	2	7
β-strand	229-230	2	7
β-strand	232-233	2	1
α-helix	266-274	9
α-helix	290-300	11
α-helix	310-318	9
α-helix	322-325	4
α-helix	327-329	3
α-helix	330-334	5
α-helix	342-354	13
α-helix	356-359	4
α-helix	362-367	6
α-helix	374-387	14
α-helix	396-401	6
α-helix	402-405	4
α-helix	409-412	4
α-helix	477-483	7
α-helix	487-500	14
α-helix	504-509	6
α-helix	511-528	18
α-helix	533-560	28
α-helix	566-577	12
α-helix	580-583	4
β-strand	591-592	2	8
β-strand	600-604	5	8
β-strand	610-611	2	8
α-helix	618	1
β-strand	619-625	7	8
β-strand	630-637	8	8
α-helix	642-660	19
β-strand	672-674	3	8
β-strand	679-683	5	8
β-strand	688-689	2	9
α-helix	690-696	7
α-helix	700-707	8
β-strand	709	1	10
α-helix	714-716	3
β-strand	717	1	10
α-helix	719-738	20
β-strand	749-751	3	9
β-strand	757-759	3	9
α-helix	781-785	5
α-helix	793-810	18
α-helix	813-821	9
α-helix	829-832	4
α-helix	838-846	9
α-helix	852-867	16
α-helix	868-870	3

Chain B: 73 helices, 49 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	18-21	4
β-strand	31-34	4	11
β-strand	39-44	6	11
β-strand	49-56	8	11
α-helix	65-77	13
β-strand	84	1	12
β-strand	89-91	3	11
β-strand	98-104	7	11
β-strand	108-109	2	12
α-helix	110-114	5
α-helix	119-120	2
α-helix	122-140	19
α-helix	151-153	3
β-strand	154-156	3	12
β-strand	162-164	3	12
β-strand	175-176	2	13
α-helix	183-186	4
β-strand	194	1	14
α-helix	199-201	3
β-strand	202-203	2	13
α-helix	205-212	8
α-helix	229-232	4
α-helix	239-252	14
β-strand	260	1	14
α-helix	261-268	8
α-helix	277-280	4
α-helix	284-293	10
α-helix	298-300	3
α-helix	304-310	7
β-strand	312	1	15
β-strand	316	1	15
α-helix	318-319	2
α-helix	320-324	5
α-helix	325-328	4
α-helix	329-332	4
α-helix	339-348	10
α-helix	350-357	8
α-helix	375-383	9
α-helix	392-404	13
α-helix	406-408	3
α-helix	411-417	7
α-helix	419-424	6
α-helix	425-427	3
α-helix	431-444	14
α-helix	445-447	3
α-helix	458	1
α-helix	459-463	5
α-helix	464-466	3
α-helix	468-472	5
α-helix	476-483	8
α-helix	486-509	24
α-helix	524-545	22
α-helix	550-559	10
α-helix	561-567	7
α-helix	569-573	5
α-helix	574-578	5
α-helix	579-582	4
α-helix	583-586	4
α-helix	591-608	18
α-helix	610-614	5
α-helix	617-623	7
α-helix	631-645	15
α-helix	650-660	11
α-helix	661-665	5
α-helix	669-685	17
α-helix	689-690	2
α-helix	691-695	5
α-helix	696-699	4
α-helix	700-702	3
β-strand	703	1	16
β-strand	720	1	16
α-helix	721-722	2
α-helix	726-733	8
α-helix	738-752	15
α-helix	760-762	3
α-helix	765-777	13
α-helix	782-789	8
α-helix	791-808	18
α-helix	809-811	3
β-strand	818-819	2	6
α-helix	826-828	3
β-strand	829	1	1
α-helix	939-961	23
α-helix	965-967	3
α-helix	974-976	3
β-strand	985-989	5	17
β-strand	996-1001	6	18
β-strand	1007-1012	6	18
β-strand	1017-1021	5	18
β-strand	1036-1038	3	18
β-strand	1045-1051	7	19
β-strand	1056-1061	6	19
β-strand	1065-1071	7	19
α-helix	1072	1
β-strand	1082-1089	8	19
β-strand	1100-1105	6	20
β-strand	1110-1115	6	20
β-strand	1120-1125	6	20
β-strand	1134-1136	3	20
α-helix	1139-1141	3
β-strand	1144-1149	6	21
β-strand	1155-1160	6	21
β-strand	1164-1169	6	21
β-strand	1175-1180	6	21
β-strand	1187-1192	6	22
β-strand	1200-1204	5	22
β-strand	1209-1212	4	22
β-strand	1222-1225	4	22
α-helix	1230	1
β-strand	1242-1248	7	23
β-strand	1255-1260	6	23
β-strand	1265-1269	5	23
α-helix	1273-1275	3
β-strand	1277-1278	2	23
α-helix	1285-1287	3
β-strand	1288-1295	8	22
β-strand	1298-1305	8	22
α-helix	1322-1325	4
β-strand	1332-1339	8	17
β-strand	1343-1349	7	17
β-strand	1354-1357	4	17

Chain C: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	111-127	17
β-strand	136	1	24
α-helix	139-169	31
α-helix	178-190	13
α-helix	194-216	23
α-helix	219-259	41
α-helix	264-266	3
α-helix	269-273	5
β-strand	276-279	4	25
β-strand	282-285	4	25
β-strand	288-290	3	25
α-helix	300-321	22
α-helix	323-325	3
β-strand	328-331	4	26
α-helix	334-336	3
β-strand	338-341	4	26
β-strand	349-350	2	26
α-helix	358-360	3
α-helix	364-383	20
β-strand	396-397	2	27
β-strand	402-404	3	27
β-strand	412-414	3	27
α-helix	422-446	25

Chain D: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	42	1	28
β-strand	49	1	28
β-strand	54	1	24
α-helix	56-61	6
α-helix	75-98	24
α-helix	101-106	6
α-helix	110-176	67
α-helix	180-204	25
β-strand	208-210	3	29
β-strand	261-263	3	29
β-strand	269-270	2	29
α-helix	276-279	4
α-helix	280-283	4
α-helix	298-321	24
α-helix	331-333	3
α-helix	341-361	21
α-helix	366-368	3
α-helix	374-382	9

Chain E: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	30
α-helix	25-32	8
β-strand	47-55	9	30
β-strand	58-66	9	30
α-helix	71-73	3
β-strand	87-92	6	30
α-helix	96-100	5
α-helix	102-108	7
α-helix	109-113	5
β-strand	119-124	6	30
α-helix	136-143	8
β-strand	150-152	3	30
β-strand	154	1	31
β-strand	159	1	31
α-helix	161-168	8
α-helix	170-175	6

Chain L: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	7-22	16
α-helix	27-41	15
α-helix	52-90	39

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, I	protein	450	Homo sapiens	Q14457 (AlphaFold model)
Beclin 1-associated autophagy-related key regulator	D	protein	493	Homo sapiens	Q6ZNE5 (AlphaFold model)
Ras-related protein Rab-1A	E	protein	207	Homo sapiens	P62820
Nuclear receptor-binding factor 2	L	protein	308	Homo sapiens	Q96F24

Sequence of entity 1 (A), FASTA

>9RX4_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

>9RX4_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, I), FASTA

>9RX4_3 Beclin-1 (chains C, I)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Sequence of entity 4 (D), FASTA

>9RX4_4 Beclin 1-associated autophagy-related key regulator (chains D)
MTASPSGKGARALEAPGCGPRPLARDLVDSVDDAEGLYVAVERCPLCNTTRRRLTCAKCV
QSGDFVYFDGRDRERFIDKKERLSRLKSKQEEFQKEVLKAMEGKWITDQLRWKIMSCKMR
IEQLKQTICKGNEEMEKNSEGLLKTKEKNQKLYSRAQRHQEKKEKIQRHNRKLGDLVEKK
TIDLRSHYERLANLRRSHILELTSVIFPIEEVKTGVRDPADVSSESDSAMTSSTVSKLAE
ARRTTYLSGRWVCDDHSGDTSISITGPWISLPNNGDYSAYYSWVEEKKTTQGPDMEQSNP
AYTISAALCYATQLVNILSHILDVNLPKKLCNSEFCGENLSKQKFTRAVKKLNANILYLC
FSQHVNLDQLQPLHTLRNLMYLVSPSSEHLGRSGPFEVRADLEESMEFVDPGVAGESDES
GDERVSDEETDLGTDWENLPSPRFCDIPSQSVEVSQSQSTQASPPIASSSAGGMISSAAA
SVTSWFKAYTGHR

Sequence of entity 5 (E), FASTA

>9RX4_5 Ras-related protein Rab-1A (chains E)
GSHMSSMNPEYDYLFKLLLIGDSGVGKSSLLLRFADDTYTESYISTIGVDFKIRTIELDG
KTIKLQIWDTAGLERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENV
NKLLVGNKSDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRMG
PGATAGGAEKSNVKIQSTPVKQSGGGC

Sequence of entity 6 (L), FASTA

>9RX4_6 Nuclear receptor-binding factor 2 (chains L)
MAHHHHHHSSGSENLYFQGSHMEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAA
YLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQREERLKAQQNTDKDAAAHLQ
TSHKPSAEDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPDTLLYLLQQKSEPAEPCIGSK
APKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGPIEKELDVDA
DFVETSELWSLPPHAETATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSED
ILKGFMNN

Ligands and cofactors

ID	Name	Formula	Copies
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
ZN	Zinc ion	Zn	2

Primary citation

When VPS34 complexes double down: Two RAB5s for VPS34-CII, two RAB1s for NRBF2-dimerized VPS34-CI. Spokaite, S., Ohashi, Y., Dessus, A.N. et al. 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…

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