3WAO: Atg13 LIR-fused human LC3B_2-119

Crystal structure of Atg13 LIR-fused human LC3B_2-119. Determined by X-ray diffraction at 2.6 Å resolution. Released 25 Dec 2013.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,113
Mol. weight: 62.22 kDa
Released: 25 Dec 2013

Explore 3WAO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WAO contains 18 α-helices and 26 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	23-26	4
α-helix	29-42	14
β-strand	46-53	8	1
β-strand	67-71	5	1
β-strand	75	1	2
α-helix	76-86	11
β-strand	96-99	4	1
β-strand	102-103	2	1
β-strand	110	1	2
α-helix	111-118	8
β-strand	125-130	6	1

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	3
α-helix	29-42	14
β-strand	46-53	8	4
β-strand	67-71	5	4
β-strand	75	1	5
α-helix	76-86	11
β-strand	96-99	4	4
β-strand	110	1	5
α-helix	111-118	8
β-strand	125-130	6	4

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
α-helix	29-42	14
β-strand	46-53	8	3
α-helix	60-63	4
β-strand	67-71	5	3
β-strand	75	1	6
α-helix	76-86	11
β-strand	96-99	4	3
β-strand	110	1	6
α-helix	111-118	8
β-strand	125-130	6	3

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	23-26	4
α-helix	29-42	14
β-strand	46-53	8	7
α-helix	61-63	3
β-strand	67-71	5	7
α-helix	76-87	12
β-strand	96-99	4	7
β-strand	102-103	2	7
α-helix	111-118	8
β-strand	125-130	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B	A, B, C, D	protein	134	Homo sapiens	O75143 (AlphaFold model), Q9GZQ8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3WAO_1 Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3B (chains A, B, C, D)
GSSSGNTHDDFVMIGSPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLP
VLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDE
DGFLYMVYASQETF

Primary citation

Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism. Suzuki, H., Tabata, K., Morita, E. et al. Structure (2014) 22:47-58. DOI 10.1016/j.str.2013.09.023 · 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
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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