9MHG: Cryo EM reconstruction of PI3KC3-C1

Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation. Determined by electron microscopy at 3.2 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 5
Atoms: 22,624
Mol. weight: 394.36 kDa
Ligands: MYR, MG, GTP
Released: 12 Feb 2025

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

Secondary structure: helices and β-sheets

9MHG contains 132 α-helices and 98 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: 64 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	10-14	5
α-helix	17-22	6
β-strand	27-34	8	1
β-strand	39-45	7	1
β-strand	48-56	9	1
α-helix	64-78	15
β-strand	84-85	2	2
β-strand	89-95	7	1
β-strand	98-104	7	1
β-strand	108-109	2	2
α-helix	110-113	4
α-helix	119	1
α-helix	122-142	21
β-strand	154-156	3	2
β-strand	162-165	4	2
β-strand	175-176	2	3
α-helix	181-182	2
α-helix	183-187	5
β-strand	194	1	4
α-helix	199-201	3
β-strand	202-203	2	3
α-helix	205-207	3
α-helix	229-232	4
α-helix	234-236	3
α-helix	237-253	17
β-strand	260	1	4
α-helix	261-268	8
α-helix	275-278	4
α-helix	284-293	10
α-helix	298-300	3
α-helix	304-311	8
β-strand	312	1	5
β-strand	316	1	5
α-helix	318-319	2
α-helix	320-324	5
α-helix	325-332	8
α-helix	339-357	19
α-helix	375-383	9
α-helix	392-405	14
α-helix	411-412	2
α-helix	413-418	6
α-helix	419-425	7
α-helix	431-445	15
α-helix	458	1
α-helix	459-463	5
α-helix	464-467	4
α-helix	470-472	3
α-helix	476-507	32
α-helix	526-545	20
α-helix	550-572	23
α-helix	573-578	6
α-helix	579-584	6
α-helix	591-608	18
α-helix	611-623	13
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
β-strand	703	1	6
α-helix	713-718	6
β-strand	720	1	6
α-helix	721-725	5
α-helix	726-733	8
α-helix	738-752	15
α-helix	760-762	3
α-helix	765-776	12
α-helix	781-789	9
α-helix	791-805	15
α-helix	808-811	4
β-strand	820	1	7
α-helix	826-828	3
β-strand	829-832	4	8
α-helix	939-967	29
α-helix	974-976	3
β-strand	985-989	5	9
β-strand	996-1001	6	10
β-strand	1007-1012	6	10
β-strand	1017-1021	5	10
α-helix	1022-1024	3
β-strand	1034-1038	5	10
β-strand	1045-1050	6	11
β-strand	1056-1061	6	11
β-strand	1065-1072	8	11
β-strand	1081-1089	9	11
β-strand	1098-1105	8	12
β-strand	1110-1116	7	12
β-strand	1120-1125	6	12
β-strand	1131-1136	6	12
α-helix	1139-1141	3
β-strand	1144-1149	6	13
β-strand	1155-1160	6	13
β-strand	1164-1169	6	13
β-strand	1174-1180	7	13
β-strand	1187-1192	6	14
β-strand	1199-1204	6	14
β-strand	1210-1214	5	14
β-strand	1219-1225	7	14
β-strand	1242-1248	7	15
β-strand	1255-1260	6	15
β-strand	1266-1269	4	15
α-helix	1273-1275	3
β-strand	1277-1278	2	15
α-helix	1286-1287	2
β-strand	1299-1302	4	14
α-helix	1321-1324	4
β-strand	1332-1338	7	9
β-strand	1344-1349	6	9
β-strand	1354-1357	4	9

Chain B: 47 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	8
β-strand	18-27	10	16
α-helix	32-34	3
α-helix	35-40	6
α-helix	42-46	5
α-helix	48-51	4
β-strand	58-65	8	17
β-strand	68-69	2	17
β-strand	74-75	2	17
α-helix	76-78	3
β-strand	85-96	12	16
α-helix	97-99	3
β-strand	104-113	10	17
β-strand	119-128	10	17
β-strand	130	1	18
β-strand	135	1	8
β-strand	136	1	18
α-helix	137	1
β-strand	140-145	6	16
β-strand	146-147	2	17
α-helix	150-152	3
β-strand	160	1	17
α-helix	171-183	13
α-helix	188-189	2
α-helix	191-211	21
β-strand	215-221	7	16
β-strand	225-226	2	7
β-strand	229-230	2	7
β-strand	232-234	3	8
α-helix	265-274	10
α-helix	277-279	3
α-helix	282-284	3
α-helix	290-300	11
α-helix	307-309	3
α-helix	310-318	9
α-helix	320-323	4
α-helix	329-336	8
α-helix	342-352	11
α-helix	356-358	3
α-helix	360-367	8
α-helix	374-384	11
α-helix	389-394	6
α-helix	396-402	7
α-helix	403-405	3
α-helix	408-412	5
α-helix	475-485	11
α-helix	487-502	16
α-helix	506-509	4
α-helix	511-529	19
α-helix	533-559	27
α-helix	566-577	12
α-helix	588-590	3
β-strand	591-592	2	19
β-strand	600-604	5	19
β-strand	610-611	2	19
α-helix	618	1
β-strand	619-625	7	19
β-strand	630-637	8	19
α-helix	642-660	19
β-strand	672-676	5	19
β-strand	679-683	5	19
β-strand	688-689	2	20
α-helix	690-696	7
α-helix	700-707	8
β-strand	709	1	21
β-strand	717	1	21
α-helix	719-738	20
α-helix	746-748	3
β-strand	749-751	3	20
β-strand	757-759	3	20
α-helix	781-786	6
α-helix	793-810	18
α-helix	813-821	9
α-helix	829-832	4
α-helix	835-845	11
α-helix	852-866	15
α-helix	871-884	14

Chain C: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	57-61	5
α-helix	75-204	130
β-strand	208-210	3	22
β-strand	260-263	4	22
β-strand	269-271	3	22
α-helix	277-288	12
α-helix	299-321	23
α-helix	331-334	4
α-helix	338-340	3
α-helix	341-361	21
α-helix	374-382	9
α-helix	399-405	7

Chain D: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	139-172	34
α-helix	178-265	88
α-helix	269-273	5
β-strand	276-279	4	23
β-strand	282-285	4	23
β-strand	288-290	3	23
α-helix	300-321	22
β-strand	328-331	4	24
β-strand	338-341	4	24
β-strand	349-350	2	24
α-helix	366-384	19
β-strand	395-397	3	25
β-strand	402-404	3	25
β-strand	412-414	3	25
α-helix	422-445	24

Chain E: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	26
α-helix	24-33	10
β-strand	46-55	10	26
β-strand	58-67	10	26
α-helix	71-73	3
β-strand	86-92	7	26
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	26
α-helix	136-146	11
β-strand	150-152	3	26
β-strand	154	1	27
β-strand	159	1	27
α-helix	161-175	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphoinositide 3-kinase regulatory subunit 4	A	protein	1409	Homo sapiens	Q99570 (AlphaFold model)
Phosphatidylinositol 3-kinase catalytic subunit type 3	B	protein	887	Homo sapiens	Q8NEB9 (AlphaFold model)
Beclin 1-associated autophagy-related key regulator	C	protein	492	Homo sapiens	Q6ZNE5 (AlphaFold model)
Beclin-1	D	protein	450	Homo sapiens	Q14457 (AlphaFold model)
Ras-related protein Rab-1A	E	protein	226	Homo sapiens	P62820

Sequence of entity 1 (A), FASTA

>9MHG_1 Phosphoinositide 3-kinase regulatory subunit 4 (chains A)
MGNQLAGIAPSQILSVESYFSDIHDFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDP
TLPLTSYKQELEELKIRLNSAQNCLPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFL
NNIEKRWIAFQILTAVDQAHKSGVRHGDIKTENVMVTSWNWVLLTDFASFKPTYLPEDNP
ADFNYFFDTSRRRTCYIAPERFVDGGMFATELEYMRDPSTPLVDLNSNQRTRGELKRAMD
IFSAGCVIAELFTEGVPLFDLSQLLAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDK
RLEAEDYLKQQRGNAFPEIFYTFLQPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGH
DLPEKAEGEPKENGLVILVSVITSCLQTLKYCDSKLAALELILHLAPRLSVEILLDRITP
YLLHFSNDSVPRVRAEALRTLTKVLALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRL
AYAENIALLAETALRFLELVQLKNLNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQK
VVTLLSDPENIVKQTLMENGITRLCVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDS
IVGVAAYVGWQSSSILKPLLQQGLSDAEEFVIVKALYALTCMCQLGLLQKPHVYEFASDI
APFLCHPNLWIRYGAVGFITVVARQISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVL
KEPVSRSIFDYALRSKDITSLFRHLHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMT
EEEEDKLLALKDFMMKSNKAKANIVDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEP
DDKRARKHVKQDSNVNEEWKSMFGSLDPPNMPQALPKGSDQEVIQTGKPPRSESSAGICV
PLSTSSQVPEVTTVQNKKPVIPVLSSTILPSTYQIRITTCKTELQQLIQQKREQCNAERI
AKQMMENAEWESKPPPPGWRPKGLLVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIW
NSQKMEGKTTTTRSILTYSRIGGRVKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSP
KIHPLQSRILDQKEDGCVVDMHHFNSGAQSVLAYATVNGSLVGWDLRSSSNAWTLKHDLK
SGLITSFAVDIHQCWLCIGTSSGTMACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWV
IAAVQGNNEVSMWDMETGDRRFTLWASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAG
SDMKIRFWDLAYPERSYVVAGSTSSPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRG
PESLPVGHHDIITDVATFQTTQGFIVTASRDGIVKVWKGTENLYFQSGMAAWSHPQFEKG
GGARGGSGGGSWSHPQFEKGFDYKDDDDK

Sequence of entity 2 (B), FASTA

>9MHG_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

>9MHG_3 Beclin 1-associated autophagy-related key regulator (chains C)
MASPSGKGARALEAPGCGPRPLARDLVDSVDDAEGLYVAVERCPLCNTTRRRLTCAKCVQ
SGDFVYFDGRDRERFIDKKERLSRLKSKQEEFQKEVLKAMEGKWITDQLRWKIMSCKMRI
EQLKQTICKGNEEMEKNSEGLLKTKEKNQKLYSRAQRHQEKKEKIQRHNRKLGDLVEKKT
IDLRSHYERLANLRRSHILELTSVIFPIEEVKTGVRDPADVSSESDSAMTSSTVSKLAEA
RRTTYLSGRWVCDDHNGDTSISITGPWISLPNNGDYSAYYSWVEEKKTTQGPDMEQSNPA
YTISAALCYATQLVNILSHILDVNLPKKLCNSEFCGENLSKQKFTRAVKKLNANILYLCF
SQHVNLDQLQPLHTLRNLMYLVSPSSEHLGRSGPFEVRADLEESMEFVDPGVAGESDESG
DERVSDEETDLGTDWENLPSPRFCDIPSQSVEVSQSQSTQASPPIASSSAGGMISSAAAS
VTSWFKAYTGHR

Sequence of entity 4 (D), FASTA

>9MHG_4 Beclin-1 (chains D)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Sequence of entity 5 (E), FASTA

>9MHG_5 Ras-related protein Rab-1A (chains E)
MKSSHHHHHHENLYFQSNAMGMSSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTES
YISTIGVDFKIRTIELDGKTIKLQIWDTAGLERFRTITSSYYRGAHGIIVVYDVTDQESF
NNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNAT
NVEQSFMTMAAEIKKRMGPGATAGGAEKSNVKIQSTPVKQSGGGCC

Ligands and cofactors

ID	Name	Formula	Copies
MYR	Myristic acid	C14 H28 O2	1
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Structural pathway for PI3-kinase regulation by VPS15 in autophagy. Cook, A.S.I., Chen, M., Nguyen, T.N. et al. Science (2025) 388:eadl3787-eadl3787. DOI 10.1126/science.adl3787 · PubMed

Other PDB entries of the same protein (UniProt Q99570 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9MHF 2.73 Å, Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L)
9RX5 3.15 Å, VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L)
9RX7 3.33 Å, VPS34-CI bound to NRBF2 MIT domain (residues 1-79)
9RX6 3.52 Å, VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15…
9TW2 3.58 Å, Cryo-EM structure of human VPS34-CI in complex with GABARAP
9TW3 3.6 Å, Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation
9TZ3 3.66 Å, Cryo-EM structure of human VPS34-CI with ADP:MgF3
9RX4 3.67 Å, VPS34-CI bound to NRBF2 and RAB1A
13BV 3.77 Å, Cryo-EM structure of human PI3KC3-C1 complex
9RX8 3.87 Å, Apo VPS34-cii (VPS34/VPS15/BECLIN1/UVRAG)
9RX9 3.99 Å, VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit
9RXA 4.0 Å, VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit

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