5GTU: Vacuolar protein sorting-associated protein 29

Structural and mechanistic insights into regulation of the retromer coat by TBC1d5. Determined by X-ray diffraction at 1.5 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,812
Mol. weight: 24.14 kDa
Released: 7 Dec 2016

Explore 5GTU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GTU contains 4 α-helices and 11 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
α-helix	20-25	6
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
α-helix	96-106	11
β-strand	110-113	4	2
β-strand	119-124	6	2
β-strand	127-132	6	2
β-strand	149-156	8	1
β-strand	159-168	10	1
β-strand	171-180	10	1

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	149-155	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 29	A	protein	186	Homo sapiens	Q9UBQ0 (AlphaFold model)
TBC1 domain family member 5	B	protein	27	Homo sapiens	Q92609 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5GTU_1 Vacuolar protein sorting-associated protein 29 (chains A)
MAGHRLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDV
HIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHT
HKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVER
IEYKKP

Sequence of entity 2 (B), FASTA

>5GTU_2 TBC1 domain family member 5 (chains B)
GQQDLMINNPLSQDEGSLWNKFFQDKE

Primary citation

Structural and mechanistic insights into regulation of the retromer coat by TBC1d5. Jia, D., Zhang, J.S., Li, F. et al. Nat Commun (2016) 7:13305-13305. DOI 10.1038/ncomms13305 · PubMed

Other PDB entries of the same protein (UniProt Q9UBQ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ESE 1.35 Å, Crystal structure of human Vps29 bound to a peptide from Vps35L
6XS7 1.58 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D2
6XSA 1.83 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L2
6XS5 2.01 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1
1W24 2.1 Å, Crystal Structure Of human Vps29
8R0J 2.4 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
5WYH 2.46 Å, Crystal structure of RidL(1-200) complexed with VPS29
8R02 2.5 Å, Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl…
5OSI 2.52 Å, Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)
6XS9 2.69 Å, Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1
2R17 2.8 Å, Functional architecture of the retromer cargo-recognition complex
8SYN 2.94 Å, Human VPS35L/VPS29/VPS26C Complex

Browse structure collections

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