8ESE: Human Vps29

Crystal structure of human Vps29 bound to a peptide from Vps35L. Determined by X-ray diffraction at 1.35 Å resolution. Released 24 May 2023.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,767
Mol. weight: 23.36 kDa
Released: 24 May 2023

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

Secondary structure: helices and β-sheets

8ESE contains 5 α-helices and 14 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 X: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	25-26	2	1
α-helix	27-28	2

Chain Z: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
β-strand	11	1	2
α-helix	20-25	6
β-strand	33-36	4	1
β-strand	41	1	2
α-helix	43-52	10
β-strand	55-58	4	1
β-strand	72-77	6	3
β-strand	80-85	6	3
α-helix	96-106	11
β-strand	110-113	4	3
β-strand	120-124	5	3
β-strand	127-131	5	3
α-helix	146-148	3
β-strand	149-156	8	1
β-strand	159-168	10	1
β-strand	171-180	10	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VPS35 endosomal protein-sorting factor-like	X	protein	23	Homo sapiens	Q7Z3J2 (AlphaFold model)
Vacuolar protein sorting-associated protein 29	Z	protein	184	Homo sapiens	Q9UBQ0 (AlphaFold model)

Sequence of entity 1 (X), FASTA

>8ESE_1 VPS35 endosomal protein-sorting factor-like (chains X)
EFASCRLEAVPLEFGDYHPLKPI

Sequence of entity 2 (Z), FASTA

>8ESE_2 Vacuolar protein sorting-associated protein 29 (chains Z)
GHMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHI
VRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHK
FEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIE
YKKP

Primary citation

Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Healy, M.D., McNally, K.E., Butkovic, R. et al. Cell (2023) 186:2219-2237.e29. DOI 10.1016/j.cell.2023.04.003 · PubMed

Other PDB entries of the same protein (UniProt Q7Z3J2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SYN 2.94 Å, Human VPS35L/VPS29/VPS26C Complex
8SYO 2.94 Å, Human Retriever VPS35L/VPS29/VPS26C Complex (Composite Map)
8SYM 3.2 Å, Human VPS29/VPS35L Complex (Locally refined map)
9AU7 3.4 Å, Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map)
8P0V 6.5 Å, Structure of the human Commander complex coiled coils, DENND10 and partial Retriever…
8P0X 7.5 Å, Structure of the human Commander complex Retriever Subcomplex

Browse structure collections

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