5LXI: GABARAP-L1 ATG4B LIR Complex

GABARAP-L1 ATG4B LIR Complex. Determined by X-ray diffraction at 1.44 Å resolution. Released 8 Feb 2017.

Method: X-ray diffraction
Resolution: 1.44 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,290
Mol. weight: 32.38 kDa
Ligands: MG, PER
Released: 8 Feb 2017

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

Secondary structure: helices and β-sheets

5LXI contains 12 α-helices and 18 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 B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	11-24	14
β-strand	28-35	8	4
α-helix	42-44	3
β-strand	48-52	5	4
β-strand	56	1	5
α-helix	57-67	11
β-strand	77-79	3	4
β-strand	80	1	6
β-strand	83	1	6
α-helix	84-86	3
β-strand	90	1	5
α-helix	91-98	8
β-strand	105-110	6	4

Chains C and E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	389-390	2	1

Chain D: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	11-24	14
β-strand	28-35	8	1
α-helix	42-44	3
β-strand	48-52	5	1
β-strand	56	1	2
α-helix	57-68	12
β-strand	77-79	3	1
β-strand	80	1	3
β-strand	83	1	3
α-helix	84-86	3
β-strand	90	1	2
α-helix	91-98	8
β-strand	105-110	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor-associated protein-like 1	B, D	protein	123	Homo sapiens	Q9H0R8 (AlphaFold model)
Cysteine protease ATG4B	C, E	protein	10	Homo sapiens	Q9Y4P1 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>5LXI_1 Gamma-aminobutyric acid receptor-associated protein-like 1 (chains B, D)
GPTMGSMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSD
LTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESV
YGK

Sequence of entity 2 (C, E), FASTA

>5LXI_2 Cysteine protease ATG4B (chains C, E)
EDEDFEILSL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
PER	Peroxide ion	O2	2

Water and common crystallization additives (PGE, EDO, PEG) are not listed.

Primary citation

ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8. Skytte Rasmussen, M., Mouilleron, S., Kumar Shrestha, B. et al. Autophagy (2017) 13:834-853. DOI 10.1080/15548627.2017.1287651 · PubMed

Other PDB entries of the same protein (UniProt Q9H0R8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YOO 1.06 Å, Structure of SAMM50 LIR bound to GABARAPL1
6HOI 1.14 Å, Structure of Beclin1 LIR motif bound to GABARAPL1
6HOL 1.4 Å, Structure of ATG14 LIR motif bound to GABARAPL1
7AA7 1.45 Å, Structure of SCOC pS12/pS18 LIR motif bound to GABARAPL1
8X8A 1.53 Å, Crystal structure of STBD1 LIR motif in complex with GABARAPL1
5LXH 1.58 Å, GABARAP-L1 ATG4B LIR Complex
2R2Q 1.65 Å, Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1…
7AA9 1.72 Å, Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1
9JF2 1.76 Å, Crystal structure of GABARAPL1 in complex with ATG16L1
7JHX 1.91 Å, Crystal structure of hEPG5 LIR/GABARAPL1 complex
9HGC 2.52 Å, Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8
5DPT 2.9 Å, Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117

Browse structure collections

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