7JLP: Human ATG9A in nanodiscs

cryo-EM structure of human ATG9A in nanodiscs. Determined by electron microscopy at 3.4 Å resolution. Released 28 Oct 2020.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 3
Atoms: 12,891
Mol. weight: 234.6 kDa
Ligands: POV
Released: 28 Oct 2020

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

Secondary structure: helices and β-sheets

7JLP contains 99 α-helices and 30 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.

Chains A, B and C: 33 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	43-55	13
α-helix	60-85	26
β-strand	87	1	1
α-helix	109-111	3
α-helix	112-115	4
β-strand	116	1	1
α-helix	117-118	2
α-helix	119-126	8
α-helix	133-162	30
α-helix	163-167	5
α-helix	175-177	3
α-helix	180-189	10
α-helix	205-212	8
α-helix	214-224	11
β-strand	231-234	4	2
β-strand	238-241	4	2
α-helix	245-255	11
β-strand	263	1	3
β-strand	269	1	3
α-helix	271-274	4
α-helix	276-278	3
α-helix	279-316	38
α-helix	319-322	4
α-helix	324-327	4
β-strand	331-332	2	4
α-helix	334-339	6
α-helix	341-342	2
α-helix	347-356	10
α-helix	359-366	8
α-helix	371-397	27
α-helix	399-403	5
α-helix	405-407	3
α-helix	408-421	14
α-helix	436-445	10
α-helix	459-465	7
β-strand	469-470	2	4
α-helix	472-480	9
α-helix	482-488	7
α-helix	489-494	6
α-helix	495-497	3
α-helix	498-507	10
β-strand	509-512	4	5
β-strand	516-519	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 9A	A, B, C	protein	578	Homo sapiens	Q7Z3C6 (AlphaFold model)

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

>7JLP_1 Autophagy-related protein 9A (chains A, B, C)
MAQFDTEYQRLEASYSDSPPGEEDLLVHVAEGSKSPWHHIENLDLFFSRVYNLHQKNGFT
CMLIGEIFELMQFLFVVAFTTFLVSCVDYDILFANKMVNHSLHPTEPVKVTLPDAFLPAQ
VCSARIQENGSLITILVIAGVFWIHRLIKFIYNICCYWEIHSFYLHALRIPMSALPYCTW
QEVQARIVQTQKEHQICIHKRELTELDIYHRILRFQNYMVALVNKSLLPLRFRLPGLGEA
VFFTRGLKYNFELILFWGPGSLFLNEWSLKAEYKRGGQRLELAQRLSNRILWIGIANFLL
CPLILIWQILYAFFSYAEVLKREPGALGARCWSLYGRCYLRHFNELEHELQSRLNRGYKP
ASKYMNCFLSPLLTLLAKNGAFFAGSILAVLIALTIYDEDVLAVEHVLTTVTLLGVTVTV
CRSFIPDQHMVFCPEQLLRVILAHIHYMPDHWQGNAHRSQTRDEFAQLFQYKAVFILEEL
LSPIVTPLILIFCLRPRALEIIDFFRNFTVEVVGVGDTCSFAQMDVRQHGHPQWLSAGQT
EASVYQQAEDGKTELSLMHFAITNPGWQPPRESTAFLG

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	45

Primary citation

Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Maeda, S., Yamamoto, H., Kinch, L.N. et al. Nat Struct Mol Biol (2020) 27:1194-1201. DOI 10.1038/s41594-020-00520-2 · 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
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
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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