5D94: LC3-LIR peptide complex

Crystal structure of LC3-LIR peptide complex. Determined by X-ray diffraction at 1.53 Å resolution. Released 21 Oct 2015.

Method: X-ray diffraction
Resolution: 1.53 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,293
Mol. weight: 16.62 kDa
Released: 21 Oct 2015

Explore 5D94 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D94 contains 7 α-helices and 8 β-strands across 2 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
β-strand	30-37	8	1
α-helix	45-47	3
β-strand	51-55	5	1
β-strand	59	1	2
α-helix	60-70	11
β-strand	80-83	4	1
β-strand	86-87	2	1
β-strand	94	1	2
α-helix	95-102	8
β-strand	109-114	6	1
α-helix	116-119	4

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1281-1282	2	1
α-helix	1285-1287	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Microtubule-associated proteins 1A/1B light chain 3B	A	protein	130	Homo sapiens	Q9GZQ8 (AlphaFold model)
Peptide from FYVE and coiled-coil domain-containing protein 1	B	protein	13	Homo sapiens	Q9BQS8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5D94_1 Microtubule-associated proteins 1A/1B light chain 3B (chains A)
GPLGSMPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVP
DHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYAS
QETFGMKLSV

Sequence of entity 2 (B), FASTA

>5D94_2 Peptide from FYVE and coiled-coil domain-containing protein 1 (chains B)
DDAVFDIITDEEL

Primary citation

FYCO1 Contains a C-terminally Extended, LC3A/B-preferring LC3-interacting Region (LIR) Motif Required for Efficient Maturation of Autophagosomes during Basal Autophagy. Olsvik, H.L., Lamark, T., Takagi, K. et al. J Biol Chem (2015) 290:29361-29374. DOI 10.1074/jbc.M115.686915 · PubMed

Other PDB entries of the same protein (UniProt Q9GZQ8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Q53 1.36 Å, Crystal structure of truncated human Microtubule-associated proteins 1A/1B light chain…
6LAN 1.41 Å, Structure of CCDC50 and LC3B complex
5MS5 1.53 Å, Low-salt structure of RavZ LIR2-fused human LC3B
2ZJD 1.56 Å, Crystal Structure of LC3-p62 complex
7GAG 1.59 Å, PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with…
7GAU 1.59 Å, PanDDA analysis group deposition of ground-state model of MAP1LC3B
7ELG 1.6 Å, LC3B modificated with a covalent probe
3VTU 1.6 Å, Crystal structure of human LC3B_2-119
8Q7K 1.6 Å, IRGQ LIR2 peptide in complex with LC3B
7GAP 1.68 Å, PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with…
7GAO 1.69 Å, PanDDA analysis group deposition -- Crystal Structure of MAP1LC3B in complex with…
3VTV 1.7 Å, Crystal structure of Optineurin LIR-fused human LC3B_2-119

Browse structure collections

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