6WY6: S. cerevisiae Atg8

Crystal structure of S. cerevisiae Atg8 in complex with Ede1 (1220-1247). Determined by X-ray diffraction at 1.77 Å resolution. Released 2 Dec 2020.

Method: X-ray diffraction
Resolution: 1.77 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 2,421
Mol. weight: 33.55 kDa
Released: 2 Dec 2020

Explore 6WY6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WY6 contains 20 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 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	4
α-helix	42-44	3
β-strand	48-52	5	4
β-strand	56	1	5
α-helix	57-68	12
β-strand	77-79	3	4
β-strand	80	1	6
β-strand	83	1	6
β-strand	90	1	5
α-helix	91-98	8
α-helix	104	1
β-strand	105-110	6	4

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	11-24	14
β-strand	28-35	8	1
α-helix	42-43	2
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
β-strand	90	1	2
α-helix	91-98	8
α-helix	104	1
β-strand	105-110	6	1

Chain C: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	1221-1223	3
α-helix	1229-1234	6
α-helix	1237-1238	2
β-strand	1239-1240	2	4
α-helix	1241	1
α-helix	1243-1246	4

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	1237-1238	2
β-strand	1239-1240	2	1
α-helix	1241	1
α-helix	1243-1246	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy-related protein 8	A, B	protein	118	Saccharomyces cerevisiae	P38182 (AlphaFold model)
EH domain-containing and endocytosis protein 1	C, D	protein	28	Saccharomyces cerevisiae	P34216 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6WY6_1 Autophagy-related protein 8 (chains A, B)
GSMKSTFKSEYPFEKRKAESERIADRFPNRIPVICEKAEKSDIPEIDKRKYLVPADLTVG
QFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGENTFG

Sequence of entity 2 (C, D), FASTA

>6WY6_2 EH domain-containing and endocytosis protein 1 (chains C, D)
ADSESEFENVANAGSMEQFETIDHKDLN

Primary citation

A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits. Wilfling, F., Lee, C.W., Erdmann, P.S. et al. Mol Cell (2020) 80:764. DOI 10.1016/j.molcel.2020.10.030 · PubMed

Other PDB entries of the same protein (UniProt P38182 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RUI 1.91 Å, Crystal structure of Atg7C-Atg8 complex
3VH3 2.0 Å, Crystal structure of Atg7CTD-Atg8 complex
5YEC 2.15 Å, Crystal structure of Atg7CTD-Atg8-MgATP complex in form II
7BRN 2.23 Å, Crystal structure of Atg40 AIM fused to Atg8
6AAG 2.44 Å, Crystal structure of budding yeast Atg8 complexed with the helical AIM of Hfl1.
3VH4 2.65 Å, Crystal structure of Atg7CTD-Atg8-MgATP complex
2ZPN 2.7 Å, The crystal structure of Saccharomyces cerevisiae Atg8- Atg19(412-415) complex
3VXW 3.0 Å, Crystal structure of Saccharomyces cerevisiae Atg8 complexed with Atg32 AIM
2KQ7 Solution structure of the Autophagy-Related Protein Atg8
2KWC The NMR structure of the autophagy-related protein Atg8
2LI5 NMR structure of Atg8-Atg7C30 complex

Browse structure collections

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