9TZ3: Human VPS34-CI with ADP:MgF3

Cryo-EM structure of human VPS34-CI with ADP:MgF3. Determined by electron microscopy at 3.66 Å resolution. Released 5 Aug 2026.

Method: Electron microscopy
Resolution: 3.66 Å
Organism: Homo sapiens
Chains: 6
Atoms: 22,318
Mol. weight: 426.83 kDa
Ligands: GDP, MYR, MG, ADP
Released: 5 Aug 2026

Explore 9TZ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9TZ3 contains 134 α-helices and 98 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: 41 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7-11	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
α-helix	76-78	3
β-strand	85-96	12	2
α-helix	97-99	3
β-strand	105-113	9	3
β-strand	119-121	3	3
β-strand	125-128	4	3
β-strand	130	1	4
β-strand	135	1	1
β-strand	136	1	4
α-helix	137	1
β-strand	140-144	5	2
β-strand	160	1	3
α-helix	171-183	13
α-helix	191-204	14
β-strand	216-220	5	2
β-strand	223-226	4	5
β-strand	229-230	2	5
β-strand	232-234	3	1
α-helix	239-241	3
α-helix	269-272	4
α-helix	281-285	5
α-helix	290-299	10
α-helix	310-318	9
α-helix	323-325	3
α-helix	330-333	4
α-helix	347-350	4
α-helix	356-359	4
α-helix	365-367	3
α-helix	374-384	11
α-helix	388	1
α-helix	396-401	6
α-helix	402-405	4
α-helix	408-412	5
α-helix	475-483	9
α-helix	487-501	15
α-helix	504-509	6
α-helix	511-528	18
α-helix	533-559	27
α-helix	566-577	12
β-strand	591-592	2	6
β-strand	600-604	5	6
β-strand	610-611	2	6
β-strand	619-625	7	6
β-strand	630-637	8	6
α-helix	642-659	18
β-strand	672-674	3	6
β-strand	679-683	5	6
β-strand	688-689	2	7
α-helix	690-696	7
α-helix	700-707	8
β-strand	709	1	8
α-helix	714-716	3
β-strand	717	1	8
α-helix	719-739	21
β-strand	749-751	3	7
β-strand	757-759	3	7
α-helix	781-786	6
α-helix	793-808	16
α-helix	813-820	8
α-helix	835-837	3
α-helix	838-846	9
α-helix	854-867	14

Chain B: 67 helices, 52 β-strands

Element	Residues	Length	Sheet
α-helix	16-20	5
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	89-92	4	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	122-141	20
β-strand	154-156	3	10
β-strand	162-164	3	10
β-strand	175-176	2	11
α-helix	181-182	2
α-helix	183-187	5
β-strand	194	1	12
β-strand	202-203	2	11
α-helix	239-251	13
β-strand	260	1	12
α-helix	261-269	9
α-helix	275-278	4
α-helix	284-293	10
α-helix	298-300	3
α-helix	301-303	3
α-helix	304-310	7
β-strand	312	1	13
β-strand	316	1	13
α-helix	319	1
α-helix	320-324	5
α-helix	325-328	4
α-helix	339-348	10
α-helix	350-357	8
α-helix	375-384	10
α-helix	392-404	13
α-helix	411-417	7
α-helix	419-425	7
α-helix	431-444	14
α-helix	445-447	3
α-helix	458	1
α-helix	459-463	5
α-helix	468-470	3
α-helix	476-484	9
α-helix	486-505	20
α-helix	526-545	20
α-helix	550-559	10
α-helix	561-568	8
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	613-622	10
α-helix	623-625	3
α-helix	629-645	17
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	14
α-helix	713-718	6
β-strand	720	1	14
α-helix	722-725	4
α-helix	726-733	8
α-helix	738-752	15
α-helix	758-762	5
α-helix	765-777	13
α-helix	781-789	9
α-helix	791-800	10
α-helix	801-803	3
β-strand	818-820	3	5
α-helix	821-824	4
β-strand	829-831	3	1
α-helix	939-966	28
α-helix	973-976	4
β-strand	984-989	6	15
β-strand	996-1001	6	16
β-strand	1007-1012	6	16
β-strand	1017-1021	5	16
α-helix	1024-1026	3
β-strand	1036-1038	3	16
β-strand	1045-1050	6	17
β-strand	1056-1061	6	17
β-strand	1065-1071	7	17
β-strand	1082-1089	8	17
β-strand	1098-1101	4	18
β-strand	1104	1	18
β-strand	1111-1116	6	18
β-strand	1120-1125	6	18
β-strand	1131-1136	6	18
β-strand	1144-1149	6	19
β-strand	1155-1160	6	19
β-strand	1164-1169	6	19
β-strand	1174-1180	7	19
β-strand	1187-1192	6	20
β-strand	1199-1204	6	20
β-strand	1209-1214	6	20
β-strand	1220-1225	6	20
α-helix	1230	1
α-helix	1236-1238	3
β-strand	1242-1248	7	21
α-helix	1250-1252	3
β-strand	1255-1260	6	21
β-strand	1265-1269	5	21
α-helix	1273-1275	3
β-strand	1277-1278	2	21
β-strand	1288-1290	3	22
β-strand	1293-1295	3	20
β-strand	1298-1302	5	20
β-strand	1303-1305	3	22
α-helix	1322-1325	4
β-strand	1335-1339	5	15
β-strand	1343-1348	6	15
β-strand	1354-1358	5	15

Chain C: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	112-126	15
β-strand	136	1	23
α-helix	138-169	32
α-helix	176-215	40
α-helix	218-264	47
β-strand	277-279	3	24
β-strand	282-284	3	24
β-strand	289	1	24
α-helix	300-321	22
β-strand	328-331	4	25
β-strand	338-341	4	25
β-strand	349-350	2	25
α-helix	363-383	21
β-strand	395-397	3	26
β-strand	402-404	3	26
β-strand	412-414	3	26
α-helix	422-445	24

Chain D: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	54	1	23
α-helix	56-61	6
α-helix	75-99	25
α-helix	101-127	27
α-helix	131-151	21
α-helix	153-164	12
α-helix	167-204	38
β-strand	210-211	2	27
β-strand	260-262	3	27
β-strand	269-271	3	27
α-helix	276-278	3
α-helix	279-286	8
α-helix	294-296	3
α-helix	298-302	5
α-helix	303-321	19
α-helix	341-361	21
α-helix	366-368	3
α-helix	374-382	9
α-helix	399-401	3

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	8-23	16
α-helix	27-43	17
α-helix	51-77	27

Chain F: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	28
β-strand	24	1	28

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	1371	Homo sapiens	Q99570 (AlphaFold model)
Beclin-1	C, F	protein	450	Homo sapiens	Q14457 (AlphaFold model)
Beclin 1-associated autophagy-related key regulator	D	protein	493	Homo sapiens	Q6ZNE5 (AlphaFold model)
Nuclear receptor-binding factor 2	E	protein	84	Homo sapiens	Q96F24

Sequence of entity 1 (A), FASTA

>9TZ3_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

>9TZ3_2 Phosphoinositide 3-kinase regulatory subunit 4 (chains B)
MGNQLAGIAPSQILSVESYFSDIHDFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDP
TLPLTSYKQELEELKIRLNSAQNCLPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFL
NNIEKRWIAFQILTAVDQAHKSGVRHGDIKTENVMVTSWNWVLLTDFASFKPTYLPEDNP
ADFNYFFDTSRRRTCYIAPERFVDGGMFATELEYMRDPSTPLVDLNSNQRTRGELKRAMD
IFSAGCVIAELFTEGVPLFDLSQLLAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDK
RLEAEDYLKQQRGNAFPEIFYTFLQPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGH
DLPEKAEGEPKENGLVILVSVITSCLQTLKYCDSKLAALELILHLAPRLSVEILLDRITP
YLLHFSNDSVPRVRAEALRTLTKVLALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRL
AYAENIALLAETALRFLELVQLKNLNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQK
VVTLLSDPENIVKQTLMENGITRLCVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDS
IVGVAAYVGWQSSSILKPLLQQGLSDAEEFVIVKALYALTCMCQLGLLQKPHVYEFASDI
APFLCHPNLWIRYGAVGFITVVARQISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVL
KEPVSRSIFDYALRSKDITSLFRHLHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMT
EEEEDKLLALKDFMMKSNKAKANIVDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEP
DDKRARKHVKQDSNVNEEWKSMFGSLDPPNMPQALPKGSDQEVIQTGKPPRSESSAGICV
PLSTSSQVPEVTTVQNKKPVIPVLSSTILPSTYQIRITTCKTELQQLIQQKREQCNAERI
AKQMMENAEWESKPPPPGWRPKGLLVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIW
NSQKMEGKTTTTRSILTYSRIGGRVKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSP
KIHPLQSRILDQKEDGCVVDMHHFNSGAQSVLAYATVNGSLVGWDLRSSSNAWTLKHDLK
SGLITSFAVDIHQCWLCIGTSSGTMACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWV
IAAVQGNNEVSMWDMETGDRRFTLWASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAG
SDMKIRFWDLAYPERSYVVAGSTSSPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRG
PESLPVGHHDIITDVATFQTTQGFIVTASRDGIVKVWKSRPTTASENLYFQ

Sequence of entity 3 (C, F), FASTA

>9TZ3_3 Beclin-1 (chains C, F)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Sequence of entity 4 (D), FASTA

>9TZ3_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

>9TZ3_5 Nuclear receptor-binding factor 2 (chains E)
SHMEVMEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHL
SLELQRDSHMKQLLLIQERWKRAQ

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MYR	Myristic acid	C14 H28 O2	1
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ZN	Zinc ion	Zn	2

Primary citation

A GABARAP-PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation. Dessus, A.N., Ohashi, Y., Bourguet, M. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-76135-w · 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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