6WQZ: Autophagy-related protein 9A

Name: PDB 6WQZ: Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery
Published: 2020-07-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery. Determined by electron microscopy at 2.8 Å resolution. Released 8 Jul 2020.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 14,128
Mol. weight: 492.6 kDa
Ligands: LMN
Released: 8 Jul 2020

Explore 6WQZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WQZ contains 97 α-helices and 30 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.

Chains A and C: 30 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	43-55	13
α-helix	59-85	27
β-strand	87	1	11
α-helix	89-93	5
α-helix	112-114	3
β-strand	116	1	11
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	12
β-strand	239-241	3	12
α-helix	245-255	11
β-strand	263	1	13
β-strand	269	1	13
α-helix	271-274	4
α-helix	279-322	44
α-helix	326-328	3
β-strand	330	1	14
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	459-469	11
β-strand	471	1	14
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	15
β-strand	516-518	3	15
α-helix	521-523	3
α-helix	552-563	12
α-helix	567-570	4
α-helix	571-586	16

Chain B: 31 helices, 10 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	207-224	18
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	279-313	35
α-helix	316-322	7
α-helix	326-328	3
β-strand	330	1	9
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	459-469	11
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	10
β-strand	516-518	3	10
α-helix	521-523	3
α-helix	552-563	12
α-helix	567-570	4
α-helix	571-586	16

Chains D and E: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	690-699	10
α-helix	707-723	17

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	690-699	10
α-helix	706-722	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 9A	A, B, C, D, E, F	protein	724	Homo sapiens	Q7Z3C6 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>6WQZ_1 Autophagy-related protein 9A (chains A, B, C, D, E, F)
MAQFDTEYQRLEASYSDSPPGEEDLLVHVAEGSKSPWHHIENLDLFFSRVYNLHQKNGFT
CMLIGEIFELMQFLFVVAFTTFLVSCVDYDILFANKMVNHSLHPTEPVKVTLPDAFLPAQ
VCSARIQENGSLITILVIAGVFWIHRLIKFIYNICCYWEIHSFYLHALRIPMSALPYCTW
QEVQARIVQTQKEHQICIHKRELTELDIYHRILRFQNYMVALVNKSLLPLRFRLPGLGEA
VFFTRGLKYNFELILFWGPGSLFLNEWSLKAEYKRGGQRLELAQRLSNRILWIGIANFLL
CPLILIWQILYAFFSYAEVLKREPGALGARCWSLYGRCYLRHFNELEHELQSRLNRGYKP
ASKYMNCFLSPLLTLLAKNGAFFAGSILAVLIALTIYDEDVLAVEHVLTTVTLLGVTVTV
CRSFIPDQHMVFCPEQLLRVILAHIHYMPDHWQGNAHRSQTRDEFAQLFQYKAVFILEEL
LSPIVTPLILIFCLRPRALEIIDFFRNFTVEVVGVGDTCSFAQMDVRQHGHPQWLSAGQT
EASVYQQAEDGKTELSLMHFAITNPGWQPPRESTAFLGFLKEQVQRDGAAASLAQGGLLP
ENALFTSIQSLQSESEPLSLIANVVAGSSCRGPPLPRDLQGSRHRAEVASALRSFSPLQP
GQAPTGRAHSTMTGSGVDARTASSGSSVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXX

Ligands and cofactors

ID	Name	Formula	Copies
LMN	Lauryl Maltose Neopentyl Glycol	C47 H88 O22	6

Primary citation

Structure of Human ATG9A, the Only Transmembrane Protein of the Core Autophagy Machinery. Guardia, C.M., Tan, X.F., Lian, T. et al. Cell Rep (2020) 31:107837-107837. DOI 10.1016/j.celrep.2020.107837 · PubMed

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

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
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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