6TL0: Vacuolar protein sorting-associated protein 29

Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of VPS29 with VARP 687-747. Determined by solution NMR. Released 21 Oct 2020.

Method: Solution NMR
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 1,965
Mol. weight: 28.01 kDa
Ligands: ZN
Released: 21 Oct 2020

Explore 6TL0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TL0 contains 4 α-helices and 17 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
β-strand	11	1	2
α-helix	20-25	6
β-strand	33-36	4	1
β-strand	41	1	2
α-helix	43-52	10
β-strand	56-58	3	1
β-strand	72-77	6	3
β-strand	80-85	6	3
α-helix	96-106	11
β-strand	110-113	4	3
β-strand	120-124	5	3
β-strand	127-131	5	3
β-strand	134	1	4
β-strand	140	1	5
β-strand	143	1	5
β-strand	148	1	4
β-strand	149-155	7	1
β-strand	159-166	8	1
β-strand	173-180	8	1

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	728-731	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A	protein	192	Mus musculus	Q9QZ88 (AlphaFold model)
Ankyrin repeat domain-containing protein 27	B	protein	61	Homo sapiens	Q96NW4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6TL0_1 Vacuolar protein sorting-associated protein 29 (chains A)
GSPEFGTRDRMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLK
TLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDI
LISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGD
DVKVERIEYKKS

Sequence of entity 2 (B), FASTA

>6TL0_2 Ankyrin repeat domain-containing protein 27 (chains B)
GPLGSTEEDLEDAEDTVSAADPEFCHPLCQCPKCAPAQKRLAKVPASGLGVNVTSQDGSS
W

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29. Crawley-Snowdon, H., Yang, J.C., Zaccai, N.R. et al. Nat Commun (2020) 11:5031-5031. DOI 10.1038/s41467-020-18773-2 · 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
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

Browse structure collections

About this viewer

MolViewer shows 6TL0 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.