8TTD: VPS29

Structure of VPS29 complexed with Fam21A repeat 21 (1328-1341). Determined by X-ray diffraction at 2.01 Å resolution. Released 21 Aug 2024.

Method: X-ray diffraction
Resolution: 2.01 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 1,536
Mol. weight: 22.63 kDa
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

8TTD contains 5 α-helices and 13 β-strands across 1 chain. 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: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
β-strand	15	1	2
α-helix	24-29	6
β-strand	37-40	4	1
β-strand	45	1	2
α-helix	47-56	10
β-strand	59-62	4	1
α-helix	63-65	3
β-strand	76-81	6	3
β-strand	84-89	6	3
α-helix	100-110	11
β-strand	114-117	4	3
β-strand	124-128	5	3
β-strand	131-135	5	3
α-helix	150-152	3
β-strand	153-160	8	1
β-strand	163-172	10	1
β-strand	175-184	10	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A	protein	188	Mus musculus	Q9QZ88 (AlphaFold model)
Ser-asn-ile-phe-asp-asp-pro-leu-asn-ala-phe-gly-gly-gln	B	protein	14	Homo sapiens	Q641Q2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8TTD_1 Vacuolar protein sorting-associated protein 29 (chains A)
GSMAGHRLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAG
DVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISG
HTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKV
ERIEYKKS

Sequence of entity 2 (B), FASTA

>8TTD_2 SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN (chains B)
SNIFDDPLNAFGGQ

Primary citation

Structural basis for coupling of the WASH subunit FAM21 with the endosomal SNX27-Retromer complex. Guo, Q., Chen, K.E., Gimenez-Andres, M. et al. Proc Natl Acad Sci U S A (2024) 121:e2405041121-e2405041121. DOI 10.1073/pnas.2405041121 · 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+
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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