6KLR: Human WIPI3

Crystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A. Determined by X-ray diffraction at 2.21 Å resolution. Released 29 Apr 2020.

Method: X-ray diffraction
Resolution: 2.21 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,485
Mol. weight: 76.92 kDa
Released: 29 Apr 2020

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

Secondary structure: helices and β-sheets

6KLR contains 3 α-helices and 31 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: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	1
β-strand	21-26	6	1
β-strand	29-34	6	1
β-strand	39-44	6	1
β-strand	53-55	3	2
β-strand	57	1	3
β-strand	59	1	3
β-strand	62-66	5	2
β-strand	72-77	6	2
β-strand	82-88	7	2
β-strand	93-99	7	4
β-strand	102-107	6	4
β-strand	110-115	6	4
β-strand	122-127	6	4
β-strand	137-138	2	5
β-strand	146-150	5	5
α-helix	156	1
β-strand	157-161	5	5
α-helix	168-169	2
β-strand	170-172	3	5
β-strand	179-184	6	6
β-strand	190-195	6	6
β-strand	200-205	6	6
β-strand	211-216	6	6
β-strand	224-229	6	7
β-strand	235-240	6	7
β-strand	244-249	6	7
β-strand	260-262	3	7
β-strand	271-274	4	8
β-strand	280-284	5	8
β-strand	289-295	7	8
β-strand	301-308	8	8

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1380-1383	4	2
α-helix	1388-1389	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
chimera ATG2A and WIPI3	A, B	protein	350	Homo sapiens	Q2TAZ0 (AlphaFold model), Q5MNZ6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6KLR_1 chimera ATG2A and WIPI3 (chains A, B)
GPGSPRDGEPVVTQLHPGPIVVRDGYFSRPIGSTDGSPHGNGLLYAGFNQDHGCFACGME
NGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCNYLALVGGGKKKVMIWDDLKKKTVIEI
EFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPHQLHVFETCYNPKGLCVLCPNSNNSLL
AFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCIALNLQGTRIATASEKGTLIRIFDTS
SGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAEDPKSKWSFSKFQVPSG
SPCICAFGTEPNAVIAICADGSYYKFLFNPKGECIRDVYAQFLEMTDDKL

Primary citation

Multi-site-mediated entwining of the linear WIR-motif around WIPI beta-propellers for autophagy. Ren, J., Liang, R., Wang, W. et al. Nat Commun (2020) 11:2702-2702. DOI 10.1038/s41467-020-16523-y · PubMed

Other PDB entries of the same protein (UniProt Q2TAZ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SBK 1.8 Å, Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI (ATG2A).
8SBL 3.0 Å, Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI
8KBX 3.23 Å, Cryo-EM structure of human ATG2A-WIPI4 complex
8KBY 3.23 Å, Cryo-EM structure of ATG2A
8KC3 7.0 Å, Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex
8Y1L 7.05 Å, Cryo-EM structure of human N-terminally bound ATG9A-ATG2A-WIPI4 complex

Browse structure collections

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