8KBZ: Human ATG9A in LMNG micelles

Cryo-EM structure of human ATG9A in LMNG micelles. Determined by electron microscopy at 3.97 Å resolution. Released 7 Aug 2024.

Method: Electron microscopy
Resolution: 3.97 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,860
Mol. weight: 283.65 kDa
Released: 7 Aug 2024

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

Secondary structure: helices and β-sheets

8KBZ contains 82 α-helices and 32 β-strands across 3 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	43-55	13
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 9A	A, B, C	protein	839	Homo sapiens	Q7Z3C6 (AlphaFold model)

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

>8KBZ_1 Autophagy-related protein 9A (chains A, B, C)
MAQFDTEYQRLEASYSDSPPGEEDLLVHVAEGSKSPWHHIENLDLFFSRVYNLHQKNGFT
CMLIGEIFELMQFLFVVAFTTFLVSCVDYDILFANKMVNHSLHPTEPVKVTLPDAFLPAQ
VCSARIQENGSLITILVIAGVFWIHRLIKFIYNICCYWEIHSFYLHALRIPMSALPYCTW
QEVQARIVQTQKEHQICIHKRELTELDIYHRILRFQNYMVALVNKSLLPLRFRLPGLGEA
VFFTRGLKYNFELILFWGPGSLFLNEWSLKAEYKRGGQRLELAQRLSNRILWIGIANFLL
CPLILIWQILYAFFSYAEVLKREPGALGARCWSLYGRCYLRHFNELEHELQSRLNRGYKP
ASKYMNCFLSPLLTLLAKNGAFFAGSILAVLIALTIYDEDVLAVEHVLTTVTLLGVTVTV
CRSFIPDQHMVFCPEQLLRVILAHIHYMPDHWQGNAHRSQTRDEFAQLFQYKAVFILEEL
LSPIVTPLILIFCLRPRALEIIDFFRNFTVEVVGVGDTCSFAQMDVRQHGHPQWLSAGQT
EASVYQQAEDGKTELSLMHFAITNPGWQPPRESTAFLGFLKEQVQRDGAAASLAQGGLLP
ENALFTSIQSLQSESEPLSLIANVVAGSSCRGPPLPRDLQGSRHRAEVASALRSFSPLQP
GQAPTGRAHSTMTGSGVDARTASSGSSVWEGQLQSLVLSEYASTEMSLHALYMHQLHKQQ
AQAEPERHVWHRRESDESGESAPDEGGEGARAPQSIPRSASYPCAAPRPGAPETTALHGG
FQRRYGGITDPGTVPRVPSHFSRLPLGGWAEDGQSASRHPEPVPEEGSEDELPPQVHKV

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
7JLQ 4.0 Å, cryo-EM structure of human ATG9A in LMNG micelles
8KC3 7.0 Å, Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex
8Y1L 7.05 Å, Cryo-EM structure of human N-terminally bound ATG9A-ATG2A-WIPI4 complex

Browse structure collections

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