› 4qqd

X-ray diffraction
2.28Å resolution

Crystal Structure of tandem tudor domains of UHRF1 in complex with a small organic molecule

Released:
DOI: 10.2210/pdb4qqd/pdb
PDB entry 4qqd coloured by chain, front view.
PDB entry 4qqd coloured by chain, side view.
PDB entry 4qqd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II.
Liu Y, Iqbal A, Li W, Ni Z, Wang Y, Ramprasad J, Abraham KJ, Zhang M, Zhao DY, Qin S, Loppnau P, Jiang H, Guo X, Brown PJ, Zhen X, Xu G, Mekhail K, Ji X, Bedford MT, Greenblatt JF, Min J
Nat Commun 13 5453 (2022)
PMID: 36114190

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188767 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase UHRF1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 161 amino acids
Theoretical weight: 18.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96T88 (Residues: 126-285; Coverage: 20%)
Gene names: ICBP90, NP95, RNF106, UHRF1
Sequence domains: Tandem tudor domain within UHRF1
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand 36X 3 x 36X
Ligand UNX 5 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P61
Unit cell:
a: 87.338Å b: 87.338Å c: 83.921Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.2 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Tudor-dimethylarginine interactions: the condensed version.
Šimčíková et al. (2023)
4 other articles

2 mentions without citation

Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery.
Chang et al. (2021)
1 more