8DO8: Crystal structure ATG9 HDIR

Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer. Determined by X-ray diffraction at 2.41 Å resolution. Released 23 Nov 2022.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,271
Mol. weight: 147.4 kDa
Released: 23 Nov 2022

Explore 8DO8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DO8 contains 32 α-helices and 50 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 A: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
α-helix	14-16	3
α-helix	17-31	15
β-strand	33-34	2	2
α-helix	35-36	2
β-strand	37-41	5	3
β-strand	44-47	4	3
β-strand	49	1	4
β-strand	50	1	5
β-strand	52-56	5	6
β-strand	63-67	5	6
α-helix	70-86	17
β-strand	97-106	10	1
α-helix	107-109	3
α-helix	113-114	2
β-strand	115-128	14	1
α-helix	140-160	21
α-helix	166-170	5
α-helix	174-176	3
β-strand	178	1	7
β-strand	186-187	2	2
β-strand	188	1	7
α-helix	189	1
β-strand	190-194	5	1

Chain B: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	38	1	6
β-strand	42	1	4
α-helix	50-52	3
β-strand	53	1	5
α-helix	59-69	11
β-strand	75	1	8
β-strand	78	1	8
β-strand	79-88	10	9
β-strand	93-104	12	9
α-helix	113-117	5
α-helix	118-132	15
α-helix	136-142	7
β-strand	148-157	10	9
β-strand	169-177	9	9
β-strand	182-189	8	9

Chain C: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	10
α-helix	14-16	3
α-helix	17-31	15
β-strand	33-34	2	11
α-helix	35-36	2
β-strand	37-39	3	12
β-strand	44-47	4	12
β-strand	49	1	13
β-strand	50	1	14
β-strand	52-56	5	15
β-strand	63-67	5	15
α-helix	70-90	21
β-strand	95-106	12	10
α-helix	113-114	2
β-strand	115-128	14	10
α-helix	137-159	23
α-helix	166-170	5
α-helix	174-176	3
β-strand	178	1	16
β-strand	186-187	2	11
β-strand	188	1	16
α-helix	189	1
β-strand	190-196	7	10

Chain D: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	38	1	15
β-strand	42	1	13
α-helix	50-52	3
β-strand	53	1	14
α-helix	56-58	3
α-helix	59-69	11
β-strand	75	1	17
β-strand	78	1	17
β-strand	79-88	10	18
β-strand	93-103	11	18
α-helix	113-117	5
α-helix	118-132	15
α-helix	136-142	7
β-strand	148-157	10	18
β-strand	169-178	10	18
β-strand	181-189	9	18

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	837-838	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 101	A, C, E, F	protein	218	Homo sapiens	Q9BSB4 (AlphaFold model)
Autophagy-related protein 13	B, D	protein	197	Homo sapiens	O75143 (AlphaFold model)

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

>8DO8_1 Autophagy-related protein 101 (chains A, C, E, F)
GGTSEDELPPQVHKVGSDEAMNCRSEVLEVSVEGRQVEEAMLAVLHTVLLHRSTGKFHYK
KEGTYSIGTVGTQDVDCDFIDFTYVRVSSEELDRALRKVVGEFKDALRNSGGDGLGQMSL
EFYQKKKSRWPFSDECIPWEVWTVKVHVVALATEQERQICREKVGEKLCEKIINIVEVMN
RHEYLPKMPTQSEVDNVFDTGLRDVQPYLYKISFQITD

Sequence of entity 2 (B, D), FASTA

>8DO8_2 Autophagy-related protein 13 (chains B, D)
METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSSPTGSDWFNLAIKDIPE
VTHEAKKALAGQLPAVGRSMCVEISLKTSEGDSMELEIWCLEMNEKCDKEIKVSYTVYNR
LSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQTVRVGTVGTPV
GTITLSCAYRINLAFMS

Primary citation

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation. Ren, X., Nguyen, T.N., Lam, W.K. et al. Sci Adv (2023) 9:eadg2997-eadg2997. DOI 10.1126/sciadv.adg2997 · PubMed

Other PDB entries of the same protein (UniProt Q9BSB4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5C50 1.63 Å, Crystal structure of the complex of human Atg101-Atg13 HORMA domain
4WZG 1.9 Å, Structure of human ATG101
5XUY 2.2 Å, Crystal structure of ATG101-ATG13HORMA
5XV6 2.46 Å, Crystal structure of ATG101-ATG13HORMA
5XV1 2.51 Å, Crystal structure of ATG101-ATG13HORMA
5XV3 2.57 Å, Crystal structure of ATG101-ATG13HORMA
5XV4 2.95 Å, Crystal structure of ATG101-ATG13HORMA

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