8KC3: Autophagy-related protein 9A

Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex. Determined by electron microscopy at 7.0 Å resolution. Released 7 Aug 2024.

Method: Electron microscopy
Resolution: 7.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 15,687
Mol. weight: 536.67 kDa
Released: 7 Aug 2024

Explore 8KC3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8KC3 contains 107 α-helices and 131 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: 26 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	43-55	13
α-helix	59-85	27
β-strand	87	1	1
α-helix	89-93	5
α-helix	112-114	3
β-strand	116	1	1
α-helix	117-118	2
α-helix	119-127	9
α-helix	130-162	33
α-helix	163-168	6
α-helix	180-193	14
α-helix	207-224	18
β-strand	231-233	3	2
β-strand	239-241	3	2
α-helix	245-255	11
β-strand	263	1	3
β-strand	269	1	3
α-helix	271-274	4
α-helix	279-322	44
α-helix	326-328	3
β-strand	330	1	4
α-helix	334-337	4
α-helix	347-356	10
α-helix	358-365	8
α-helix	371-397	27
α-helix	405-424	20
α-helix	435-445	11
α-helix	450-452	3
α-helix	459-469	11
β-strand	471	1	4
α-helix	472-480	9
α-helix	482-492	11
α-helix	495-497	3
α-helix	498-507	10
β-strand	510-512	3	5
β-strand	516-518	3	5

Chain B: 29 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	44-55	12
α-helix	59-85	27
β-strand	87	1	6
α-helix	89-93	5
α-helix	112-114	3
β-strand	116	1	6
α-helix	117-118	2
α-helix	119-127	9
α-helix	130-162	33
α-helix	163-168	6
α-helix	180-193	14
α-helix	201-203	3
α-helix	206-224	19
β-strand	231-233	3	7
β-strand	239-241	3	7
α-helix	245-255	11
β-strand	263	1	8
β-strand	269	1	8
α-helix	271-274	4
α-helix	279-312	34
α-helix	313-317	5
α-helix	318-322	5
α-helix	326-328	3
β-strand	330	1	9
α-helix	334-337	4
α-helix	347-356	10
α-helix	358-367	10
α-helix	371-397	27
β-strand	402	1	10
β-strand	404	1	10
α-helix	407-424	18
α-helix	426-427	2
α-helix	434-445	12
α-helix	459-466	8
β-strand	471	1	9
α-helix	472-480	9
α-helix	482-492	11
α-helix	495-497	3
α-helix	498-507	10
β-strand	510-512	3	11
β-strand	516-518	3	11

Chain C: 27 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	44-55	12
α-helix	59-85	27
β-strand	87	1	12
α-helix	89-93	5
α-helix	112-114	3
β-strand	116	1	12
α-helix	117-118	2
α-helix	119-127	9
α-helix	130-162	33
α-helix	163-168	6
α-helix	180-193	14
α-helix	202-203	2
α-helix	207-224	18
β-strand	231-233	3	13
β-strand	239-241	3	13
α-helix	245-255	11
β-strand	263	1	14
β-strand	269	1	14
α-helix	271-274	4
α-helix	279-322	44
α-helix	326-328	3
β-strand	330	1	15
α-helix	334-337	4
α-helix	347-356	10
α-helix	358-365	8
α-helix	371-397	27
α-helix	407-424	18
α-helix	434-445	12
α-helix	450-452	3
α-helix	459-466	8
β-strand	471	1	15
α-helix	472-480	9
α-helix	482-492	11
α-helix	495-497	3
α-helix	498-507	10
β-strand	510-512	3	16
β-strand	516-518	3	16

Chain D: 11 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-8	3
β-strand	9-14	6	17
β-strand	20-25	6	17
β-strand	28-33	6	17
β-strand	38-43	6	17
α-helix	45-48	4
β-strand	49-56	8	18
β-strand	62-72	11	18
β-strand	78-83	6	18
α-helix	91-94	4
β-strand	95-100	6	18
β-strand	105-111	7	19
β-strand	114-119	6	19
β-strand	122-127	6	19
β-strand	134-139	6	19
β-strand	149-150	2	20
β-strand	158-162	5	20
β-strand	168-173	6	20
α-helix	178	1
β-strand	186-189	4	20
β-strand	195-200	6	21
β-strand	206-211	6	21
β-strand	216-221	6	21
β-strand	227-232	6	21
β-strand	240-245	6	22
β-strand	251-256	6	22
β-strand	260-265	6	22
α-helix	269-271	3
β-strand	273-274	2	21
α-helix	276-278	3
α-helix	288-291	4
α-helix	293	1
β-strand	294-295	2	21
α-helix	296	1
β-strand	298-301	4	22
β-strand	308-312	5	23
β-strand	317	1	24
β-strand	320	1	24
β-strand	321-327	7	23
β-strand	331-337	7	23
β-strand	343-350	8	23
α-helix	351-353	3

Chain E: 14 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	278-279	2	25
α-helix	294-303	10
β-strand	425	1	26
β-strand	428-429	2	25
β-strand	436	1	27
α-helix	452-462	11
β-strand	487	1	28
β-strand	490	1	27
β-strand	498-499	2	29
β-strand	502	1	26
β-strand	513-514	2	29
β-strand	522	1	28
β-strand	541	1	30
β-strand	559	1	29
β-strand	594	1	30
α-helix	601-608	8
β-strand	632-634	3	31
β-strand	643	1	30
β-strand	679-682	4	31
β-strand	692-695	4	31
β-strand	738-740	3	31
α-helix	797-806	10
β-strand	814	1	32
β-strand	817	1	33
α-helix	829-838	10
β-strand	926	1	34
β-strand	929	1	32
β-strand	932	1	33
β-strand	935	1	35
β-strand	962	1	35
β-strand	965	1	33
β-strand	966-967	2	36
β-strand	968	1	32
β-strand	971	1	34
α-helix	973-975	3
β-strand	979-981	3	37
β-strand	984-985	2	36
β-strand	986	1	38
α-helix	1043-1044	2
β-strand	1045	1	38
β-strand	1051-1053	3	37
β-strand	1060	1	39
β-strand	1064	1	37
β-strand	1065	1	40
β-strand	1068	1	41
α-helix	1083-1091	9
α-helix	1106	1
β-strand	1107	1	39
α-helix	1108	1
β-strand	1112	1	40
β-strand	1115	1	41
β-strand	1116-1117	2	42
β-strand	1121	1	43
β-strand	1133	1	44
β-strand	1134	1	43
β-strand	1138-1139	2	42
β-strand	1141-1142	2	45
β-strand	1151-1157	7	45
β-strand	1161	1	46
β-strand	1164	1	44
β-strand	1182	1	44
β-strand	1184-1185	2	47
β-strand	1186	1	46
β-strand	1190-1196	7	45
β-strand	1219-1220	2	47
α-helix	1224-1236	13
β-strand	1418	1	48
β-strand	1422	1	49
β-strand	1425-1427	3	50
β-strand	1484-1486	3	50
β-strand	1487-1489	3	49
β-strand	1493	1	48
β-strand	1523-1525	3	49
β-strand	1528	1	51
β-strand	1540	1	51
β-strand	1558	1	49
α-helix	1596-1607	12
β-strand	1676	1	52
α-helix	1692-1699	8
β-strand	1706	1	52
α-helix	1723-1727	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 9A	A, B, C	protein	839	Homo sapiens	Q7Z3C6 (AlphaFold model)
WD repeat domain phosphoinositide-interacting protein 4	D	protein	360	Homo sapiens	Q9Y484 (AlphaFold model)
Autophagy-related protein 2 homolog A	E	protein	1938	Homo sapiens	Q2TAZ0 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8KC3_1 Autophagy-related protein 9A (chains A, B, C)
MAQFDTEYQRLEASYSDSPPGEEDLLVHVAEGSKSPWHHIENLDLFFSRVYNLHQKNGFT
CMLIGEIFELMQFLFVVAFTTFLVSCVDYDILFANKMVNHSLHPTEPVKVTLPDAFLPAQ
VCSARIQENGSLITILVIAGVFWIHRLIKFIYNICCYWEIHSFYLHALRIPMSALPYCTW
QEVQARIVQTQKEHQICIHKRELTELDIYHRILRFQNYMVALVNKSLLPLRFRLPGLGEA
VFFTRGLKYNFELILFWGPGSLFLNEWSLKAEYKRGGQRLELAQRLSNRILWIGIANFLL
CPLILIWQILYAFFSYAEVLKREPGALGARCWSLYGRCYLRHFNELEHELQSRLNRGYKP
ASKYMNCFLSPLLTLLAKNGAFFAGSILAVLIALTIYDEDVLAVEHVLTTVTLLGVTVTV
CRSFIPDQHMVFCPEQLLRVILAHIHYMPDHWQGNAHRSQTRDEFAQLFQYKAVFILEEL
LSPIVTPLILIFCLRPRALEIIDFFRNFTVEVVGVGDTCSFAQMDVRQHGHPQWLSAGQT
EASVYQQAEDGKTELSLMHFAITNPGWQPPRESTAFLGFLKEQVQRDGAAASLAQGGLLP
ENALFTSIQSLQSESEPLSLIANVVAGSSCRGPPLPRDLQGSRHRAEVASALRSFSPLQP
GQAPTGRAHSTMTGSGVDARTASSGSSVWEGQLQSLVLSEYASTEMSLHALYMHQLHKQQ
AQAEPERHVWHRRESDESGESAPDEGGEGARAPQSIPRSASYPCAAPRPGAPETTALHGG
FQRRYGGITDPGTVPRVPSHFSRLPLGGWAEDGQSASRHPEPVPEEGSEDELPPQVHKV

Sequence of entity 2 (D), FASTA

>8KC3_2 WD repeat domain phosphoinositide-interacting protein 4 (chains D)
MTQQPLRGVTSLRFNQDQSCFCCAMETGVRIYNVEPLMEKGHLDHEQVGSMGLVEMLHRS
NLLALVGGGSSPKFSEISVLIWDDAREGKDSKEKLVLEFTFTKPVLSVRMRHDKIVIVLK
NRIYVYSFPDNPRKLFEFDTRDNPKGLCDLCPSLEKQLLVFPGHKCGSLQLVDLASTKPG
TSSAPFTINAHQSDIACVSLNQPGTVVASASQKGTLIRLFDTQSKEKLVELRRGTDPATL
YCINFSHDSSFLCASSDKGTVHIFALKDTRLNRRSALARVGKVGPMIGQYVDSQWSLASF
TVPAESACICAFGRNTSKNVNSVIAICVDGTFHKYVFTPDGNCNREAFDVYLDICDDDDF

Sequence of entity 3 (E), FASTA

>8KC3_3 Autophagy-related protein 2 homolog A (chains E)
MSRWLWPWSNCVKERVCRYLLHHYLGHFFQEHLSLDQLSLDLYKGSVALRDIHLEIWSVN
EVLESMESPLELVEGFVGSIEVAVPWAALLTDHCTVRVSGLQLTLQPRRGPAPGAADSQS
WASCMTTSLQLAQECLRDGLPEPSEPPQPLEGLEMFAQTIETVLRRIKVTFLDTVVRVEH
SPGDGERGVAVEVRVQRLEYCDEAVRDPSQAPPVDVHQPPAFLHKLLQLAGVRLHYEELP
AQEEPPEPPLQIGSCSGYMELMVKLKQNEAFPGPKLEVAGQLGSLHLLLTPRQLQQLQEL
LSAVSLTDHEGLADKLNKSRPLGAEDLWLIEQDLNQQLQAGAVAEPLSPDPLTNPLLNLD
NTDLFFSMAGLTSSVASALSELSLSDVDLASSVRSDMASRRLSAQAHPAGKMAPNPLLDT
MRPDSLLKMTLGGVTLTLLQTSAPSSGPPDLATHFFTEFDATKDGPFGSRDFHHLRPRFQ
RACPCSHVRLTGTAVQLSWELRTGSRGRRTTSMEVHFGQLEVLECLWPRGTSEPEYTEIL
TFPGTLGSQASARPCAHLRHTQILRRVPKSRPRRSVACHCHSELALDLANFQADVELGAL
DRLAALLRLATVPAEPPAGLLTEPLPAMEQQTVFRLSAPRATLRLRFPIADLRPEPDPWA
GQAVRAEQLRLELSEPQFRSELSSGPGPPVPTHLELTCSDLHGIYEDGGKPPVPCLRVSK
ALDPKSTGRKYFLPQVVVTVNPQSSSTQWEVAPEKGEELELSVESPCELREPEPSPFSSK
RTMYETEEMVIPGDPEEMRTFQSRTLALSRCSLEVILPSVHIFLPSKEVYESIYNRINND
LLMWEPADLLPTPDPAAQPSGFPGPSGFWHDSFKMCKSAFKLANCFDLTPDSDSDDEDAH
FFSVGASGGPQAAAPEAPSLHLQSTFSTLVTVLKGRITALCETKDEGGKRLEAVHGELVL
DMEHGTLFSVSQYCGQPGLGYFCLEAEKATLYHRAAVDDYPLPSHLDLPSFAPPAQLAPT
IYPSEEGVTERGASGRKGQGRGPHMLSTAVRIHLDPHKNVKEFLVTLRLHKATLRHYMAL
PEQSWHSQLLEFLDVLDDPVLGYLPPTVITILHTHLFSCSVDYRPLYLPVRVLITAETFT
LSSNIIMDTSTFLLRFILDDSALYLSDKCEVETLDLRRDYVCVLDVDLLELVIKTWKGST
EGKLSQPLFELRCSNNVVHVHSCADSCALLVNLLQYVMSTGDLHPPPRPPSPTEIAGQKL
SESPASLPSCPPVETALINQRDLADALLDTERSLRELAQPSGGHLPQASPISVYLFPGER
SGAPPPSPPVGGPAGSLGSCSEEKEDEREEEGDGDTLDSDEFCILDAPGLGIPPRDGEPV
VTQLHPGPIVVRDGYFSRPIGSTDLLRAPAHFPVPSTRVVLREVSLVWHLYGGRDFGPHP
GHRARTGLSGPRSSPSRCSGPNRPQNSWRTQGGSGRQHHVLMEIQLSKVSFQHEVYPAEP
ATGPAAPSQELEERPLSRQVFIVQELEVRDRLASSQINKFLYLHTSERMPRRAHSNMLTI
KALHVAPTTNLGGPECCLRVSLMPLRLNVDQDALFFLKDFFTSLVAGINPVVPGETSAEA
RPETRAQPSSPLEGQAEGVETTGSQEAPGGGHSPSPPDQQPIYFREFRFTSEVPIWLDYH
GKHVTMDQVGTFAGLLIGLAQLNCSELKLKRLCCRHGLLGVDKVLGYALNEWLQDIRKNQ
LPGLLGGVGPMHSVVQLFQGFRDLLWLPIEQYRKDGRLMRGLQRGAASFGSSTASAALEL
SNRLVQAIQATAETVYDILSPAAPVSRSLQDKRSARRLRRGQQPADLREGVAKAYDTVRE
GILDTAQTICDVASRGHEQKGLTGAVGGVIRQLPPTVVKPLILATEATSSLLGGMRNQIV
PDAHKDHALKWRSDSAQD

Primary citation

Structural basis for lipid transfer by the ATG2A-ATG9A complex. Wang, Y., Dahmane, S., Ti, R. et al. Nat Struct Mol Biol (2025) 32:35-47. DOI 10.1038/s41594-024-01376-6 · PubMed

Other PDB entries of the same protein (UniProt Q7Z3C6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WQZ 2.8 Å, Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery
6WR4 2.9 Å, Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery
7JLO 3.4 Å, Cryo-EM structure of human ATG9A in amphipols
7JLP 3.4 Å, cryo-EM structure of human ATG9A in nanodiscs
8KBZ 3.97 Å, Cryo-EM structure of human ATG9A in LMNG micelles
7JLQ 4.0 Å, cryo-EM structure of human ATG9A in LMNG micelles
8Y1L 7.05 Å, Cryo-EM structure of human N-terminally bound ATG9A-ATG2A-WIPI4 complex

Browse structure collections

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