5XV4: ATG101-ATG13HORMA

Crystal structure of ATG101-ATG13HORMA. Determined by X-ray diffraction at 2.95 Å resolution. Released 4 Jul 2018.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Homo sapiens
Chains: 16
Atoms: 23,827
Mol. weight: 369.46 kDa
Released: 4 Jul 2018

Explore 5XV4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XV4 contains 114 α-helices and 196 β-strands across 16 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, C and M: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-31	24
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	79-87	9	5
β-strand	94-103	10	5
α-helix	116-131	16
α-helix	136-142	7
β-strand	149-157	9	5
α-helix	162-164	3
β-strand	169-178	10	5
β-strand	181-189	9	5

Chain B: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	6
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	70-88	19
β-strand	95-106	12	6
α-helix	113-114	2
β-strand	115-128	14	6
α-helix	134-161	28
α-helix	166-169	4
α-helix	173-176	4
β-strand	178	1	9
β-strand	186-187	2	7
β-strand	188	1	9
β-strand	190-196	7	6

Chain D: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	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	70-88	19
β-strand	95-106	12	15
α-helix	113-114	2
β-strand	115-128	14	15
α-helix	134-161	28
α-helix	166-169	4
α-helix	172-176	5
β-strand	178	1	18
β-strand	186-187	2	16
β-strand	188	1	18
β-strand	190-196	7	15

Chains E and I: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-31	24
β-strand	38	1	19
β-strand	42	1	20
α-helix	50-52	3
β-strand	53	1	21
α-helix	59-69	11
β-strand	75	1	22
β-strand	78	1	22
β-strand	79-87	9	23
β-strand	94-103	10	23
α-helix	116-131	16
α-helix	136-142	7
β-strand	149-157	9	23
α-helix	162-164	3
β-strand	169-178	10	23
β-strand	181-189	9	23

Chain F: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	24
α-helix	17-31	15
β-strand	33-34	2	25
α-helix	35-36	2
β-strand	37-39	3	26
β-strand	45-47	3	26
β-strand	49	1	20
β-strand	50	1	21
α-helix	51	1
β-strand	52-56	5	19
β-strand	63-67	5	19
α-helix	70-88	19
β-strand	95-106	12	24
α-helix	113-114	2
β-strand	115-129	15	24
α-helix	134-158	25
α-helix	166-169	4
α-helix	172-176	5
β-strand	178	1	27
β-strand	186-187	2	25
β-strand	188	1	27
β-strand	190-196	7	24
β-strand	202-203	2	14

Chains G and K: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-31	24
β-strand	38	1	28
β-strand	42	1	29
α-helix	50-52	3
β-strand	53	1	30
α-helix	56-58	3
α-helix	59-69	11
β-strand	75	1	31
β-strand	78	1	31
β-strand	79-87	9	32
β-strand	93-103	11	32
α-helix	116-131	16
α-helix	136-142	7
β-strand	149-157	9	32
α-helix	162-164	3
β-strand	169-178	10	32
β-strand	181-189	9	32

Chain H: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	33
α-helix	17-31	15
β-strand	33-34	2	34
α-helix	35-36	2
β-strand	37-39	3	35
β-strand	45-47	3	35
β-strand	49	1	29
β-strand	50	1	30
β-strand	52-56	5	28
β-strand	63-67	5	28
α-helix	70-88	19
β-strand	95-106	12	33
α-helix	113-114	2
β-strand	115-128	14	33
α-helix	134-158	25
α-helix	166-169	4
α-helix	173-176	4
β-strand	178	1	36
β-strand	186-187	2	34
β-strand	188	1	36
β-strand	190-196	7	33
β-strand	202-203	2	5
α-helix	206-209	4

Chain J: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	42
α-helix	17-31	15
β-strand	33-34	2	43
α-helix	35-36	2
β-strand	37-39	3	44
β-strand	45-47	3	44
β-strand	49	1	38
β-strand	50	1	39
β-strand	52-56	5	37
β-strand	63-67	5	37
α-helix	70-88	19
β-strand	95-106	12	42
α-helix	113-114	2
β-strand	115-128	14	42
α-helix	134-161	28
α-helix	166-169	4
α-helix	172-176	5
β-strand	178	1	45
β-strand	186-187	2	43
β-strand	188	1	45
β-strand	190-196	7	42
β-strand	202-203	2	46

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 13	A, C, E, G, I, K, M, O	protein	190	Homo sapiens	O75143 (AlphaFold model)
Autophagy-related protein 101	B, D, F, H, J, L, N, P	protein	218	Homo sapiens	Q9BSB4 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA

>5XV4_1 Autophagy-related protein 13 (chains A, C, E, G, I, K, M, O)
METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSSPTGSDWFNLAIKDIPE
VTHEAKKALAGQLPAVGRSMCVEISLKTSEGDSMELEIWCLEMNEKCDKEIKVSYTVYNR
LSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQTVRVGTVGTPV
GTITLSCAYR

Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA

>5XV4_2 Autophagy-related protein 101 (chains B, D, F, H, J, L, N, P)
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
5XV3 2.57 Å, Crystal structure of ATG101-ATG13HORMA
3WAO 2.6 Å, Crystal structure of Atg13 LIR-fused human LC3B_2-119
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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