› 7keo

X-ray diffraction
2.9Å resolution

Crystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment

Released:
DOI: 10.2210/pdb7keo/pdb
PDB entry 7keo coloured by chain, front view.
PDB entry 7keo coloured by chain, side view.
PDB entry 7keo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle.
Yu Y, Zheng Q, Erramilli SK, Pan M, Park S, Xie Y, Li J, Fei J, Kossiakoff AA, Liu L, Zhao M
Nat Chem Biol 17 896-905 (2021)
PMID: 34239127

Function and Biology Details

Biochemical function:
  • not assigned
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-209611 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Synthetic antigen binding fragment, heavy chain Chains: A, E
Molecule details ›
Chains: A, E
Length: 235 amino acids
Theoretical weight: 25.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
Synthetic antigen binding fragment, light chain Chains: B, F
Molecule details ›
Chains: B, F
Length: 215 amino acids
Theoretical weight: 23.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
Ubiquitin Chains: C, D, G, H
Molecule details ›
Chains: C, D, G, H
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand PO4 6 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: C2
Unit cell:
a: 186.62Å b: 43.74Å c: 174.75Å
α: 90° β: 107.81° γ: 90°
R-values:
R R work R free
0.239 0.236 0.282
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

12 review citations

Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications.
Zhong et al. (2023)
11 more

1 mention without citation

K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle.
Yu et al. (2021)