8ZQG: WIPI3

Crystal structure of WIPI3 in complex with ATG16L1. Determined by X-ray diffraction at 2.77 Å resolution. Released 1 Jan 2025.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,631
Mol. weight: 86.96 kDa
Released: 1 Jan 2025

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

Secondary structure: helices and β-sheets

8ZQG contains 6 α-helices and 59 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: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	8
β-strand	24-29	6	8
β-strand	32-37	6	8
β-strand	42-48	7	8
β-strand	53-59	7	9
β-strand	65-71	7	9
β-strand	75	1	9
β-strand	81-86	6	9
β-strand	91-97	7	9
β-strand	102-107	6	10
β-strand	111-116	6	10
β-strand	119-124	6	10
β-strand	131-136	6	10
β-strand	146-147	2	11
β-strand	155-159	5	11
β-strand	165-170	6	11
α-helix	177-178	2
β-strand	179-182	4	11
β-strand	188-193	6	12
β-strand	199-204	6	12
β-strand	209-214	6	12
β-strand	220-225	6	12
β-strand	233-238	6	13
β-strand	244-249	6	13
α-helix	250-252	3
β-strand	253-258	6	13
β-strand	287-290	4	13
β-strand	297-301	5	14
β-strand	307-312	6	14
β-strand	316-322	7	14
β-strand	328-335	8	14

Chain B: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	24-29	6	1
β-strand	32-37	6	1
β-strand	42-48	7	1
β-strand	53-59	7	2
β-strand	65-71	7	2
β-strand	75	1	2
β-strand	81-86	6	2
β-strand	91-97	7	2
β-strand	102-107	6	3
β-strand	111-116	6	3
β-strand	119-124	6	3
β-strand	131-136	6	3
β-strand	146-147	2	4
β-strand	155-159	5	4
β-strand	165-170	6	4
α-helix	177-178	2
β-strand	179-182	4	4
β-strand	188-193	6	5
β-strand	199-204	6	5
β-strand	209-214	6	5
β-strand	220-225	6	5
β-strand	233-238	6	6
β-strand	244-249	6	6
α-helix	250-252	3
β-strand	253-258	6	6
β-strand	284	1	5
β-strand	287-290	4	6
β-strand	297-301	5	7
β-strand	307-312	6	7
β-strand	316-322	7	7
β-strand	328-335	8	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	127-175	49

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	127-176	50

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WD repeat domain phosphoinositide-interacting protein 3	A, B	protein	323	Homo sapiens	Q5MNZ6 (AlphaFold model)
Autophagy-related protein 16-1	C, D	protein	69	Homo sapiens	Q676U5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8ZQG_1 WD repeat domain phosphoinositide-interacting protein 3 (chains A, B)
GPGSPHGNGLLYAGFNQDHGCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRC
NYLALVGGGKKPKYPPNKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVF
TFTHNPHQLHVFETCYNPKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPA
HEGVLSCIALNLQGTRIATASEKGTLIRIFDTSSGHLIQELRRGSQAANIYCINFNQDAS
LICVSSDHGTVHIFAAEDPKSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGSYYKFL
FNPKGECIRDVYAQFLEMTDDKL

Sequence of entity 2 (C, D), FASTA

>8ZQG_2 Autophagy-related protein 16-1 (chains C, D)
GPGSMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGK
LRKTTEENQ

Primary citation

Structure of the WIPI3/ATG16L1 Complex Reveals the Molecular Basis for the Recruitment of the ATG12~ATG5-ATG16L1 Complex by WIPI3. Gong, X., Wang, Y., Zhou, Y. et al. Cells (2024) 13. DOI 10.3390/cells13242113 · PubMed

Other PDB entries of the same protein (UniProt Q5MNZ6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6IYY 1.8 Å, Crystal structure of human WIPI3,loop deletion mutant
6KLR 2.21 Å, Crystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A
9CE3 2.9 Å, Structure of the TSC:WIPI3 lysosomal recruitment complex
9C9I 3.18 Å, Structure of the TSC1:WIPI3 complex

Browse structure collections

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