5YIS: AnkB LIR/LC3B complex

Crystal Structure of AnkB LIR/LC3B complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 23 May 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 2,231
Mol. weight: 36.03 kDa
Ligands: PO4
Released: 23 May 2018

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

Secondary structure: helices and β-sheets

5YIS contains 16 α-helices and 19 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	13-26	14
α-helix	30	1
β-strand	31-37	7	1
α-helix	45-47	3
β-strand	51-54	4	1
β-strand	59	1	2
α-helix	60-70	11
β-strand	80-83	4	1
β-strand	87	1	1
β-strand	94	1	2
α-helix	95-102	8
β-strand	109-114	6	1

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	13-26	14
β-strand	30-37	8	3
α-helix	45-47	3
β-strand	51-55	5	3
β-strand	59	1	4
α-helix	60-71	12
β-strand	80-83	4	3
β-strand	87	1	3
β-strand	94	1	4
α-helix	95-102	8
β-strand	109-114	6	3
α-helix	116-122	7
β-strand	123	1	5

Chain C: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	125-126	2	1
α-helix	129-136	8
β-strand	141	1	5
α-helix	142	1
β-strand	144	1	3

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	124-126	3	3
α-helix	127-128	2
α-helix	129-133	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Microtubule-associated proteins 1A/1B light chain 3B	A, B	protein	125	Mus musculus	Q9CQV6 (AlphaFold model)
Ankyrin-2	C, D	protein	27	Homo sapiens	Q01484 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5YIS_1 Microtubule-associated proteins 1A/1B light chain 3B (chains A, B)
MPSEKTFKQRRSFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNM
SELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESERDEDGFLYMVYASQETFG
TAMAV

Sequence of entity 2 (C, D), FASTA

>5YIS_2 Ankyrin-2 (chains C, D)
VEEEWVIVSDEEIEEARQKAPLEITEY

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins. Li, J., Zhu, R., Chen, K. et al. Nat Chem Biol (2018) 14:778-787. DOI 10.1038/s41589-018-0082-8 · PubMed

Other PDB entries of the same protein (UniProt Q9CQV6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9W1U 1.6 Å, Crystal structure of mutant apo LC3B
9W2N 1.67 Å, Crystal structure of the mutant LC3B in complex with p62
5WRD 1.9 Å, Crystal structure of LC3B in complex with FYCO1 LIR
5YIQ 2.6 Å, Crystal structure of AnkG LIR/LC3B complex

Browse structure collections

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