1Z2W: Mouse Vps29

Crystal structure of mouse Vps29 complexed with Mn2+. Determined by X-ray diffraction at 2.0 Å resolution. Released 21 Jun 2005.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,242
Mol. weight: 43.93 kDa
Ligands: MN
Released: 21 Jun 2005

Explore 1Z2W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Z2W contains 10 α-helices and 28 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	11	1	2
α-helix	20-23	4
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
β-strand	92	1	4
α-helix	96-106	11
β-strand	110-112	3	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

Chain B: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
α-helix	20-23	4
β-strand	33-36	4	5
α-helix	43-52	10
β-strand	55-58	4	5
β-strand	72-77	6	6
β-strand	80-85	6	6
α-helix	89	1
β-strand	90	1	4
α-helix	91	1
α-helix	96-106	11
β-strand	110-112	3	6
β-strand	120-124	5	6
β-strand	127-131	5	6
β-strand	140	1	7
β-strand	143	1	7
α-helix	146-148	3
β-strand	149-156	8	5
β-strand	159-168	10	5
β-strand	171-180	10	5

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>1Z2W_1 Vacuolar protein sorting 29 (chains A, B)
GSPEFGTRDRMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLK
TLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDI
LISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGD
DVKVERIEYKKS

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	4

Water and common crystallization additives (GOL) are not listed.

Primary citation

Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly. Collins, B.M., Skinner, C.F., Watson, P.J. et al. Nat Struct Mol Biol (2005) 12:594-602. DOI 10.1038/nsmb954 · 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)
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)
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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