3PSN: Mouse VPS29

Crystal structure of mouse VPS29 complexed with Mn2+. Determined by X-ray diffraction at 2.4 Å resolution. Released 15 Dec 2010.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Mus musculus
Chains: 2
Atoms: 2,956
Mol. weight: 43.58 kDa
Ligands: MN
Released: 15 Dec 2010

Explore 3PSN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PSN contains 6 α-helices and 24 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: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
α-helix	20-23	4
β-strand	33-36	4	1
α-helix	43-52	10
β-strand	55-58	4	1
β-strand	72-77	6	2
β-strand	80-85	6	2
β-strand	91	1	3
α-helix	96-106	11
β-strand	110-113	4	2
β-strand	120-124	5	2
β-strand	127-131	5	2
β-strand	149-156	8	1
β-strand	159-168	10	1
β-strand	171-180	10	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
α-helix	20-23	4
β-strand	33-36	4	4
α-helix	43-52	10
β-strand	55-58	4	4
β-strand	72-77	6	5
β-strand	80-85	6	5
β-strand	91	1	3
α-helix	96-106	11
β-strand	110-113	4	5
β-strand	120-124	5	5
β-strand	127-131	5	5
β-strand	149-156	8	4
β-strand	159-168	10	4
β-strand	171-180	10	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, B	protein	192	Mus musculus	Q9QZ88 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3PSN_1 Vacuolar protein sorting-associated protein 29 (chains A, B)
GSPEFGTRDRMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLK
TLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDI
LISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGD
DVKVERIEYKKS

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	6

Primary citation

Conformational dynamics and biomolecular interactions of VPS29 studied by NMR and X-ray crystallography. Swarbrick, J., Shaw, D., Chhabra, S. et al. To be published.

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
9O9I 2.35 Å, Crystal structure of mouse Vps29 bound to DENND4C peptide (re-refinement)
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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