5XV3: ATG101-ATG13HORMA

Crystal structure of ATG101-ATG13HORMA. Determined by X-ray diffraction at 2.57 Å resolution. Released 4 Jul 2018.

Method: X-ray diffraction
Resolution: 2.57 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,900
Mol. weight: 92.47 kDa
Released: 4 Jul 2018

Explore 5XV3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XV3 contains 31 α-helices and 48 β-strands across 4 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: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	38	1	1
β-strand	42	1	2
α-helix	50-52	3
β-strand	53	1	3
α-helix	56-58	3
α-helix	59-69	11
β-strand	75	1	4
β-strand	78	1	4
β-strand	79-88	10	5
β-strand	93-103	11	5
α-helix	115-131	17
α-helix	136-142	7
β-strand	148-157	10	5
α-helix	162-164	3
β-strand	169-178	10	5
β-strand	181-189	9	5

Chain B: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	6
α-helix	14-16	3
α-helix	17-31	15
β-strand	33-34	2	7
α-helix	35-36	2
β-strand	37-39	3	8
β-strand	45-47	3	8
β-strand	49	1	2
β-strand	50	1	3
α-helix	51	1
β-strand	52-56	5	1
β-strand	63-67	5	1
α-helix	70-89	20
β-strand	96-106	11	6
α-helix	113-114	2
β-strand	115-129	15	6
α-helix	134-159	26
α-helix	166-169	4
α-helix	174-176	3
β-strand	178	1	9
β-strand	186-187	2	7
β-strand	188	1	9
β-strand	190-195	6	6
α-helix	197-199	3

Chain C: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-31	24
β-strand	38	1	10
β-strand	42	1	11
α-helix	50-52	3
β-strand	53	1	12
α-helix	59-69	11
β-strand	75	1	13
β-strand	78	1	13
β-strand	79-88	10	14
β-strand	93-103	11	14
α-helix	114-131	18
α-helix	136-142	7
β-strand	148-157	10	14
β-strand	169-179	11	14
β-strand	181-189	9	14

Chain D: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	15
α-helix	14-16	3
α-helix	17-31	15
β-strand	33-34	2	16
α-helix	35-36	2
β-strand	37-39	3	17
β-strand	45-47	3	17
β-strand	49	1	11
β-strand	50	1	12
β-strand	52-56	5	10
β-strand	63-67	5	10
α-helix	70-89	20
β-strand	96-106	11	15
α-helix	113-114	2
β-strand	115-129	15	15
α-helix	134-161	28
α-helix	166-170	5
α-helix	174-176	3
β-strand	178	1	18
β-strand	186-187	2	16
β-strand	188	1	18
β-strand	190-196	7	15
α-helix	197-199	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 13	A, C	protein	190	Homo sapiens	O75143 (AlphaFold model)
Autophagy-related protein 101	B, D	protein	218	Homo sapiens	Q9BSB4 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5XV3_1 Autophagy-related protein 13 (chains A, C)
METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSSPTGSDWFNLAIKDIPE
VTHEAKKALAGQLPAVGRSMCVEISLKTSEGDSMELEIWCLEMNEKCDKEIKVSYTVYNR
LSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQTVRVGTVGTPV
GTITLSCAYR

Sequence of entity 2 (B, D), FASTA

>5XV3_2 Autophagy-related protein 101 (chains B, D)
MNCRSEVLEVSVEGRQVEEAMLAVLHTVLLHRSTGKFHYAAAGTYSIGTVGTQDVDCDFI
DFTYVRVSSEELDRALRKVVGEFKDALRNSGGDGLGQMSLEFYQKKKSRWPFSDECIPWE
VWTVKVHVVALATEQERQICREKVGEKLCEKIINIVEVMNRHEYLPKMPTQSEVDNVFDT
GLRDVQPYLYKISFQITDALGTSVTTTMRRLIKDTLAL

Primary citation

The C-terminal region of ATG101 bridges ULK1 and PtdIns3K complex in autophagy initiation. Kim, B.-W., Jin, Y., Kim, J. et al. Autophagy (2018) 14:2104-2116. DOI 10.1080/15548627.2018.1504716 · PubMed

Other PDB entries of the same protein (UniProt O75143 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HYN 1.14 Å, Structure of ATG13 LIR motif bound to GABARAP
5C50 1.63 Å, Crystal structure of the complex of human Atg101-Atg13 HORMA domain
5XUY 2.2 Å, Crystal structure of ATG101-ATG13HORMA
8DO8 2.41 Å, Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer
5XV6 2.46 Å, Crystal structure of ATG101-ATG13HORMA
5XV1 2.51 Å, Crystal structure of ATG101-ATG13HORMA
3WAO 2.6 Å, Crystal structure of Atg13 LIR-fused human LC3B_2-119
5XV4 2.95 Å, Crystal structure of ATG101-ATG13HORMA
8SOI 4.2 Å, Structure of human ULK1 complex core (2:1:1 stoichiometry)
8SRM 4.46 Å, Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant
8SQZ 5.85 Å, Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture
9C82 6.84 Å, Structure of human ULK1C:PI3KC3-C1 supercomplex

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