2KDI: Ubiquitin/UIM fusion protein

Solution structure of a Ubiquitin/UIM fusion protein. Determined by solution NMR. Released 9 Feb 2010.

Method: Solution NMR
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 904
Mol. weight: 12.87 kDa
Released: 9 Feb 2010

Explore 2KDI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2KDI contains 6 α-helices and 8 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	1
β-strand	21-25	5	1
β-strand	31	1	2
α-helix	32-43	12
α-helix	47-49	3
β-strand	50-52	3	1
β-strand	53-54	2	3
β-strand	57-58	2	3
α-helix	59-60	2
β-strand	64	1	2
β-strand	75-80	6	1
α-helix	95-102	8
α-helix	106-110	5
α-helix	111-113	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein	A	protein	114	Saccharomyces cerevisiae	P40343 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2KDI_1 Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein (chains A)
MHHHHHHGEFQIFAKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIWAGKQLE
DGRTLSDYNIQRESTLHLVLRLRGGSMGGAADEEELIRKAIELSLKESRNSGGY

Primary citation

Conformational Dynamics and Structural Plasticity Play Critical Roles in the Ubiquitin Recognition of a UIM Domain. Sgourakis, N.G., Patel, M.M., Garcia, A.E. et al. J Mol Biol (2010) 396:1128-1144. DOI 10.1016/j.jmb.2009.12.052 · PubMed

Other PDB entries of the same protein (UniProt P40343 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1VFY 1.15 Å, Phosphatidylinositol-3-phosphate binding fyve domain of VPS27P protein from…
1O06 1.45 Å, Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)
3R42 1.87 Å, Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide
6NJG 2.35 Å, Ubiquitin Variant in Complex with Ubiquitin Interacting Motif
2PJW 3.01 Å, The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting
1Q0V Solution Structure of Tandem UIMs of Vps27
1Q0W Solution structure of Vps27 amino-terminal UIM-ubiquitin complex

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