6HOH: VPS34 LIR motif

Structure of VPS34 LIR motif (S249E) bound to GABARAP. Determined by X-ray diffraction at 2.25 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,362
Mol. weight: 61.08 kDa
Released: 27 Feb 2019

Explore 6HOH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HOH contains 26 α-helices and 33 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-7--4	4
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	57-65	9
β-strand	77-79	3	1
β-strand	80	1	3
β-strand	83	1	3
β-strand	90	1	2
α-helix	91-98	8
β-strand	105-110	6	1

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-15--11	5
α-helix	-7--3	5
α-helix	4-8	5
α-helix	11-24	14
β-strand	28-35	8	4
β-strand	48-52	5	4
β-strand	56	1	5
α-helix	57-65	9
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

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	-10--8	3	4
α-helix	4-8	5
α-helix	11-24	14
β-strand	28-35	8	7
α-helix	42-44	3
β-strand	48-52	5	7
β-strand	56	1	8
α-helix	57-66	10
β-strand	77-79	3	7
β-strand	80	1	9
β-strand	83	1	9
α-helix	84-86	3
β-strand	90	1	8
α-helix	91-98	8
β-strand	105-110	6	7

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-7--4	4
α-helix	4-8	5
α-helix	11-24	14
β-strand	28-35	8	10
α-helix	42-44	3
β-strand	48-52	5	10
β-strand	56	1	11
α-helix	57-65	9
β-strand	77-79	3	10
β-strand	80	1	12
β-strand	83	1	12
α-helix	84-86	3
β-strand	90	1	11
α-helix	91-98	8
β-strand	105-110	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated…	A, B, C, D	protein	129	Homo sapiens	O95166 (AlphaFold model), Q8NEB9 (AlphaFold model)

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

>6HOH_1 Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein (chains A, B, C, D)
SPILTEFELVKVPDPGSMKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGD
LDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDF
FLYIAYSDE

Primary citation

Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs. Birgisdottir, A.B., Mouilleron, S., Bhujabal, Z. et al. Autophagy (2019) 15:1333-1355. DOI 10.1080/15548627.2019.1581009 · PubMed

Other PDB entries of the same protein (UniProt O95166 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HYO 1.07 Å, Structure of ULK1 LIR motif bound to GABARAP
6YOP 1.1 Å, Structure of SAMM50 LIR bound to GABARAP
7ZKR 1.1 Å, Human GABARAP in complex with stapled peptide Pen3-ortho
6HYN 1.14 Å, Structure of ATG13 LIR motif bound to GABARAP
7AA8 1.25 Å, Structure of SCOC LIR bound to GABARAP
6HOG 1.26 Å, Structure of VPS34 LIR motif bound to GABARAP
8T2M 1.27 Å, Crystal structure of GABARAP in complex with the LIR of NSs4
3D32 1.3 Å, Complex of GABA(A) receptor-associated protein (GABARAP) with a synthetic peptide
6HB9 1.3 Å, Crystal structure of the GABARAP in complex with the UBA5 LIR motif
7BRQ 1.4 Å, Crystal structure of human FAM134B LIR fused to human GABARAP
9I9X 1.42 Å, Human GABARAP in complex with artificial peptide IM-2
9HGD 1.5 Å, Crystal structure of human GABARAP in complex with cyclic peptide GAB_D23

Browse structure collections

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