1P3Q: Vacuolar protein sorting-associated protein VPS9

Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9. Determined by X-ray diffraction at 1.7 Å resolution. Released 24 Jun 2003.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Saccharomyces cerevisiae, Bos taurus
Chains: 4
Atoms: 1,958
Mol. weight: 29.22 kDa
Released: 24 Jun 2003

Explore 1P3Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P3Q contains 13 α-helices and 14 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 Q: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	401-419	19
α-helix	425-434	10
α-helix	441-443	3

Chain R: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	425-435	11
α-helix	439-448	10

Chain U: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Chain V: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-71	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein VPS9	Q, R	protein	54	Saccharomyces cerevisiae	P54787 (AlphaFold model)
Ubiquitin	U, V	protein	76	Bos taurus	P0CH28 (AlphaFold model)

Sequence of entity 1 (Q, R), FASTA

>1P3Q_1 Vacuolar protein sorting-associated protein VPS9 (chains Q, R)
SSLIKKIEENERKDTLNTLQNMFPDMDPSLIEDVCIAAASRIGPCVDALLSLSE

Sequence of entity 2 (U, V), FASTA

>1P3Q_2 Ubiquitin (chains U, V)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Mechanism of Ubiquitin Recognition by the CUE Domain of Vps9p. Prag, G., Misra, S., Jones, E.A. et al. Cell (2003) 113:609-620. DOI 10.1016/S0092-8674(03)00364-7 · PubMed

Other PDB entries of the same protein (UniProt P54787 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MN3 2.3 Å, Cue domain of yeast Vps9p

Browse structure collections

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