7BL1: Human complex II-BATS

human complex II-BATS bound to membrane-attached Rab5a-GTP. Determined by electron microscopy at 9.8 Å resolution. Released 3 Mar 2021.

Method: Electron microscopy
Resolution: 9.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 15,071
Mol. weight: 407.58 kDa
Ligands: MG, GTP
Released: 3 Mar 2021

Explore 7BL1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BL1 contains 126 α-helices and 106 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 AAA: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	65-66	2	1
β-strand	70	1	2
β-strand	78	1	2
β-strand	81-82	2	1
β-strand	112-116	5	3
β-strand	130-134	5	3
α-helix	135-137	3
β-strand	145-146	2	4
β-strand	149	1	5
β-strand	155	1	5
β-strand	158-159	2	4
α-helix	174-184	11
α-helix	194-229	36
α-helix	235-281	47
α-helix	282-286	5
α-helix	289-328	40
α-helix	360-365	6
α-helix	368-375	8
β-strand	394-395	2	6
α-helix	407-409	3
β-strand	410-411	2	6
α-helix	415-417	3
α-helix	418-440	23

Chain BBB: 42 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	7
β-strand	19-26	8	8
α-helix	44-47	4
α-helix	48-50	3
β-strand	57-64	8	9
β-strand	65	1	10
β-strand	68	1	10
α-helix	72-73	2
β-strand	74-75	2	9
α-helix	81-83	3
β-strand	89-93	5	8
α-helix	97-99	3
β-strand	105-112	8	9
β-strand	123-128	6	9
α-helix	136-139	4
β-strand	142-143	2	8
β-strand	150	1	9
α-helix	170-183	14
α-helix	192-211	20
β-strand	217-221	5	8
β-strand	230	1	7
α-helix	238-240	3
α-helix	264-277	14
α-helix	292-300	9
β-strand	307-308	2	11
α-helix	309	1
α-helix	312-318	7
α-helix	320-325	6
α-helix	330-336	7
α-helix	342-354	13
α-helix	362-367	6
α-helix	374-383	10
α-helix	390-394	5
α-helix	399-402	4
α-helix	403-405	3
α-helix	408-412	5
α-helix	475-483	9
α-helix	487-501	15
α-helix	504-509	6
α-helix	513-529	17
α-helix	534-561	28
α-helix	566-576	11
α-helix	577-581	5
α-helix	582-587	6
α-helix	591	1
β-strand	592-593	2	12
β-strand	596-600	5	12
β-strand	601	1	13
β-strand	610-611	2	14
β-strand	619-620	2	14
β-strand	621-624	4	15
β-strand	625	1	13
β-strand	630-636	7	15
α-helix	642-660	19
β-strand	672-674	3	15
β-strand	680-683	4	15
α-helix	691-696	6
α-helix	700-707	8
α-helix	720-739	20
β-strand	749-751	3	16
β-strand	757-759	3	16
α-helix	781-789	9
α-helix	791-795	5
α-helix	796-812	17
α-helix	814-823	10
α-helix	835-845	11
α-helix	854-867	14
α-helix	869-871	3

Chain CCC: 54 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	17
β-strand	38-46	9	17
β-strand	49-54	6	17
α-helix	55	1
α-helix	68-78	11
β-strand	89	1	18
α-helix	91-93	3
β-strand	102	1	18
α-helix	110-116	7
α-helix	123-142	20
α-helix	152-154	3
β-strand	157	1	19
β-strand	163	1	19
β-strand	183-184	2	11
α-helix	201-206	6
α-helix	238-254	17
α-helix	261-268	8
α-helix	279-282	4
α-helix	284-295	12
α-helix	304-309	6
α-helix	315-332	18
α-helix	333-335	3
α-helix	337-354	18
α-helix	378-386	9
α-helix	393-403	11
α-helix	410-416	7
α-helix	418-426	9
α-helix	433-446	14
α-helix	454-457	4
α-helix	458-473	16
α-helix	477-505	29
α-helix	528-557	30
β-strand	561-563	3	20
β-strand	566-568	3	20
α-helix	570-572	3
α-helix	573-579	7
α-helix	581-587	7
α-helix	591-608	18
α-helix	612-616	5
α-helix	618-621	4
α-helix	627-638	12
α-helix	649-660	12
α-helix	665-679	15
α-helix	684-686	3
α-helix	687-693	7
α-helix	695-698	4
α-helix	708-717	10
α-helix	730-732	3
α-helix	740-748	9
α-helix	749-751	3
α-helix	760-767	8
α-helix	776-779	4
α-helix	783-786	4
α-helix	788-791	4
α-helix	792-795	4
α-helix	799-815	17
β-strand	969	1	21
α-helix	974-976	3
β-strand	985-990	6	22
α-helix	995	1
β-strand	996	1	23
β-strand	1000-1001	2	24
α-helix	1004-1006	3
β-strand	1008-1011	4	24
β-strand	1012	1	23
β-strand	1016	1	25
β-strand	1017-1020	4	24
α-helix	1022-1027	6
β-strand	1037	1	24
β-strand	1040	1	25
β-strand	1045-1050	6	26
α-helix	1051	1
β-strand	1054	1	21
β-strand	1057-1061	5	26
β-strand	1066-1072	7	26
β-strand	1083-1090	8	26
β-strand	1097-1104	8	27
β-strand	1110-1116	7	27
β-strand	1121-1125	5	27
β-strand	1130-1135	6	27
α-helix	1139-1141	3
β-strand	1144-1149	6	28
β-strand	1155-1160	6	28
β-strand	1165-1169	5	28
β-strand	1174-1179	6	28
α-helix	1185-1187	3
β-strand	1190-1192	3	29
β-strand	1198-1201	4	29
β-strand	1208-1210	3	30
β-strand	1213-1214	2	29
β-strand	1219	1	29
β-strand	1224-1225	2	30
α-helix	1238-1241	4
β-strand	1245-1247	3	31
β-strand	1254-1259	6	31
β-strand	1264-1269	6	31
β-strand	1288-1289	2	32
β-strand	1292	1	30
β-strand	1295	1	33
β-strand	1298	1	33
β-strand	1301-1302	2	30
β-strand	1304-1305	2	32
β-strand	1332-1338	7	22
β-strand	1344-1349	6	22
β-strand	1353-1357	5	22

Chain DDD: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	17-26	10	38
α-helix	33-42	10
α-helix	49-52	4
β-strand	55-64	10	38
β-strand	67-76	10	38
α-helix	80-85	6
α-helix	86-90	5
β-strand	95-101	7	38
α-helix	105-121	17
β-strand	127-133	7	38
α-helix	135-140	6
α-helix	145-153	9
β-strand	158-161	4	38
α-helix	170-180	11

Chain EEE: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	114-122	9
α-helix	123-127	5
α-helix	129-177	49
α-helix	182-250	69
α-helix	254-267	14
β-strand	276-279	4	34
β-strand	282-285	4	34
β-strand	288-290	3	34
α-helix	300-321	22
β-strand	328-331	4	35
β-strand	333	1	36
β-strand	335	1	36
β-strand	338-341	4	35
α-helix	342-344	3
β-strand	350	1	35
α-helix	358-361	4
α-helix	364-384	21
β-strand	394-395	2	37
β-strand	402-405	4	37
β-strand	412-414	3	37
α-helix	426-448	23

Chain FFF: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	-6-5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UV radiation resistance-associated gene protein	AAA	protein	699	Homo sapiens	Q9P2Y5 (AlphaFold model)
Phosphatidylinositol 3-kinase catalytic subunit type 3	BBB	protein	887	Homo sapiens	Q8NEB9 (AlphaFold model)
Phosphoinositide 3-kinase regulatory subunit 4	CCC	protein	1371	Homo sapiens	Q99570 (AlphaFold model)
Beclin-1	EEE	protein	450	Homo sapiens	Q14457 (AlphaFold model)
unknown peptide	FFF	protein	22	Homo sapiens
Ras-related protein Rab-5A	DDD	protein	168	Homo sapiens	P20339

Sequence of entity 1 (AAA), FASTA

>7BL1_1 UV radiation resistance-associated gene protein (chains AAA)
MSASASVGGPVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQ
LLDTYFTLHLCSTEKIYKEFYRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGG
KENIYQLLIEWKVCLDGLKYLGQQIHARNQNEIIFGLNDGYYGAPFEHKGYSNAQKTILL
QVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECL
QLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKEC
TAKRELFLKTNAQLTIRCRQLLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSI
AVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNINDKLTEKEREFPLYPKGGEKL
QFDYGVYLLNKNIAQLRYQHGLGTPDLRQTLPNLKNFMEHGLMVRCDRHHTSSAIPVPKR
QSSIFGGADVGFSGGIPSPDKGHRKRASSENERLQYKTPPPSYNSALAQPVTTVPSMGET
ERKITSLSSSLDTSLDFSKENKKKGEDLVGSLNGGHANVHPSQEQGEALSGHRATVNGTL
LPSEQAGSASVQLPGEFHPVSEAELCCTVEQAEEIIGLEATGFASGDQLEAFNCIPVDSA
VAVECDEQVLGEFEEFSRRIYALNENVSSFRRPRRSSDK

Sequence of entity 2 (BBB), FASTA

>7BL1_2 Phosphatidylinositol 3-kinase catalytic subunit type 3 (chains BBB)
MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLYVT
CQVFAEGKPLALPVRTSYKAFSTRWNWNEWLKLPVKYPDLPRNAQVALTIWDVYGPGKAV
PVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTPGRTSSTLSEDQMSRLAKLTK
AHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYGIVYYEKDG
DESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNAATRDQLNIIV
SYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDV
EDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKK
DSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLI
SRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRS
LLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVK
IRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRK
ENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAE
VMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLN
KEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVK
KVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIHKFAQYWRK

Sequence of entity 3 (CCC), FASTA

>7BL1_3 Phosphoinositide 3-kinase regulatory subunit 4 (chains CCC)
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 4 (EEE), FASTA

>7BL1_4 Beclin-1 (chains EEE)
MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEE
ETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTG
DLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSEQL
QMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ
LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEW
NEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFF
WDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFN
SEEQWTKALKFMLTNLKWGLAWVSSQFYNK

Sequence of entity 5 (FFF), FASTA

>7BL1_5 unknown peptide (chains FFF)
AAAAAAAAAAAAAAAAAAAAAA

Sequence of entity 6 (DDD), FASTA

>7BL1_6 Ras-related protein Rab-5A (chains DDD)
NKISQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVSLDDTTVKFEIWD
TAGLERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKA
DLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes. Tremel, S., Ohashi, Y., Morado, D.R. et al. Nat Commun (2021) 12:1564-1564. DOI 10.1038/s41467-021-21695-2 · PubMed

Other PDB entries of the same protein (UniProt Q9P2Y5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9ZPD 3.38 Å, Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus
9ZPC 3.83 Å, Cryo-EM structure of human PI3KC3-C2

Browse structure collections

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