9O9I: Mouse Vps29

Crystal structure of mouse Vps29 bound to DENND4C peptide (re-refinement). Determined by X-ray diffraction at 2.35 Å resolution. Released 13 Aug 2025.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 1,616
Mol. weight: 23.2 kDa
Ligands: CAC
Released: 13 Aug 2025

Explore 9O9I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9O9I contains 4 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 A: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	4	1
β-strand	5-10	6	1
α-helix	24-29	6
β-strand	37-40	4	1
α-helix	47-56	10
β-strand	60-62	3	1
β-strand	76-81	6	2
β-strand	84-89	6	2
α-helix	100-110	11
β-strand	114-117	4	2
β-strand	123-127	5	2
β-strand	132-136	5	2
β-strand	144	1	3
β-strand	147	1	3
β-strand	153-160	8	1
β-strand	163-172	10	1
β-strand	175-184	10	1

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1195-1196	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Vacuolar protein sorting-associated protein 29	A	protein	188	Mus musculus	Q9QZ88 (AlphaFold model)
Ala-lys-val-val-gln-arg-glu-asp-val-glu-thr-gly-leu-asp-pro-leu-ser-leu	B	protein	18	Homo sapiens	Q5VZ89 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9O9I_1 Isoform 2 of Vacuolar protein sorting-associated protein 29 (chains A)
GSMAGHRLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAG
DVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISG
HTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKV
ERIEYKKS

Sequence of entity 2 (B), FASTA

>9O9I_2 ALA-LYS-VAL-VAL-GLN-ARG-GLU-ASP-VAL-GLU-THR-GLY-LEU-ASP-PRO-LEU-SER-LEU (chains B)
AKVVQREDVETGLDPLSL

Ligands and cofactors

ID	Name	Formula	Copies
CAC	Cacodylate ion	C2 H6 As O2	1

Primary citation

Mapping of endosomal proximity proteomes reveals Retromer as a hub for RAB GTPase regulation. Anton-Plagaro, C., Chen, K.E., Guo, Q. et al. Nat Commun (2025) 16:6990-6990. DOI 10.1038/s41467-025-61802-1 · PubMed

Other PDB entries of the same protein (UniProt Q9QZ88 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FUD 1.68 Å, Crystal structure of Vps29 in complex with Chaetomium thermophilum Vps5 (71 to 80)
1Z2W 2.0 Å, Crystal structure of mouse Vps29 complexed with Mn2+
8TTD 2.01 Å, Structure of VPS29 complexed with Fam21A repeat 21 (1328-1341)
1Z2X 2.22 Å, Crystal structure of mouse Vps29
3PSN 2.4 Å, Crystal structure of mouse VPS29 complexed with Mn2+
8TTC 3.01 Å, Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 20 (1289-1302)
3PSO 3.2 Å, Crystal structure of mouse VPS29 complexed with Zn2+
8TTA 3.46 Å, Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 21 (1328-1341)
6VAB 4.9 Å, Mouse retromer sub-structure: VPS35/VPS35 flat dimer
7U6F 4.9 Å, Mouse retromer (VPS26/VPS35/VPS29) heterotrimers
6VAC 5.7 Å, Mouse retromer (VPS26/VPS35/VPS29) heterotrimer
6TL0 Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of…

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