› 5ohl

X-ray diffraction
2.5Å resolution

K6-specific affimer bound to K6 diUb

Released:
DOI: 10.2210/pdb5ohl/pdb
PDB entry 5ohl coloured by chain, front view.
PDB entry 5ohl coloured by chain, side view.
PDB entry 5ohl coloured by chain, top view.
Source organisms:
Primary publication:
Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling.
Michel MA, Swatek KN, Hospenthal MK, Komander D
Mol Cell 68 233-246.e5 (2017)
PMID: 28943312

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143306 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
K6-specific affimer Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 116 amino acids
Theoretical weight: 13.22 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
Ubiquitin Chains: I, J, K, L, M, N, O, P
Molecule details ›
Chains: I, J, K, L, M, N, O, P
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand 15P 4 x 15P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P1
Unit cell:
a: 60.502Å b: 69.672Å c: 99.297Å
α: 79.79° β: 79.76° γ: 83.08°
R-values:
R R work R free
0.202 0.2 0.227
Expression system: Escherichia coli

Quick links

Citations

39 review citations

Building and decoding ubiquitin chains for mitophagy.
Harper et al. (2018)
38 more

2 mentions without citation

Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling.
Michel et al. (2017)
1 more