8FUD: Vps29

Crystal structure of Vps29 in complex with Chaetomium thermophilum Vps5 (71 to 80). Determined by X-ray diffraction at 1.68 Å resolution. Released 24 Jul 2024.

Method: X-ray diffraction
Resolution: 1.68 Å
Organisms: Mus musculus, Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Chains: 4
Atoms: 3,441
Mol. weight: 44.5 kDa
Ligands: PO4
Released: 24 Jul 2024

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

Secondary structure: helices and β-sheets

8FUD contains 8 α-helices and 23 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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
α-helix	24-29	6
β-strand	37-40	4	1
α-helix	47-56	10
β-strand	59-62	4	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	124-128	5	2
β-strand	131-135	5	2
β-strand	153-160	8	1
β-strand	163-172	10	1
β-strand	175-184	10	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	3
α-helix	24-29	6
β-strand	37-40	4	3
α-helix	47-56	10
β-strand	60-62	3	3
β-strand	70	1	2
β-strand	76-81	6	4
β-strand	84-89	6	4
α-helix	100-110	11
β-strand	114-117	4	4
β-strand	124-128	5	4
β-strand	131-135	5	4
β-strand	153-160	8	3
β-strand	163-172	10	3
β-strand	175-184	10	3

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	76-78	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A, B	protein	188	Mus musculus	Q9QZ88 (AlphaFold model)
Putative vacuolar protein sorting-associated protein	C, D	protein	10	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)	G0SH11 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8FUD_1 Vacuolar protein sorting-associated protein 29 (chains A, B)
GSMAGHRLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAG
DVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISG
HTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKV
ERIEYKKS

Sequence of entity 2 (C, D), FASTA

>8FUD_2 Putative vacuolar protein sorting-associated protein (chains C, D)
EDDPLGPLGA

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

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

Primary citation

Molecular basis for the assembly of the Vps5-Vps17 SNX-BAR proteins with Retromer. Chen, K.E., Tillu, V.A., Gopaldass, N. et al. bioRxiv (2024). DOI 10.1101/2024.03.24.586500

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

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)
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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