8X8A: STBD1 LIR motif

Crystal structure of STBD1 LIR motif in complex with GABARAPL1. Determined by X-ray diffraction at 1.53 Å resolution. Released 18 Sept 2024.

Method: X-ray diffraction
Resolution: 1.53 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,285
Mol. weight: 16.09 kDa
Released: 18 Sept 2024

Explore 8X8A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X8A contains 8 α-helices and 9 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, 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	36	1
β-strand	48-52	5	1
β-strand	56	1	2
α-helix	57-67	11
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

Chain B: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	202-203	2
β-strand	204-205	2	1
α-helix	206-207	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor-associated protein-like 1	A	protein	117	Homo sapiens	Q9H0R8 (AlphaFold model)
Starch-binding domain-containing protein 1	B	protein	19	Homo sapiens	O95210 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8X8A_1 Gamma-aminobutyric acid receptor-associated protein-like 1 (chains A)
MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQF
YFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK

Sequence of entity 2 (B), FASTA

>8X8A_2 Starch-binding domain-containing protein 1 (chains B)
GPGSHEEWEMVPRHSGSGS

Primary citation

Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1. Zhang, Y., Sun, Y., Shi, J. et al. Proc Natl Acad Sci U S A (2024) 121:e2402817121-e2402817121. DOI 10.1073/pnas.2402817121 · 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
5LXI 1.44 Å, GABARAP-L1 ATG4B LIR Complex
7AA7 1.45 Å, Structure of SCOC pS12/pS18 LIR motif bound to 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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