› 3clz

X-ray diffraction
2.2Å resolution

The set and ring associated (SRA) domain of UHRF1 bound to methylated DNA

Released:
DOI: 10.2210/pdb3clz/pdb
PDB entry 3clz coloured by chain, front view.
PDB entry 3clz coloured by chain, side view.
PDB entry 3clz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.
Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner C, Arrowsmith CH, Dhe-Paganon S
Nature 455 822-5 (2008)
PMID: 18772889

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 domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116139 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase UHRF1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 212 amino acids
Theoretical weight: 23.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96T88 (Residues: 413-617; Coverage: 26%)
Gene names: ICBP90, NP95, RNF106, UHRF1
Sequence domains: SAD/SRA domain
Structure domains: SRA-YDG
5'-D(*DGP*DGP*DGP*DCP*DCP*(5CM)P*DGP*DCP*DAP*DGP*DGP*DG)-3' Chains: E, G, I, K
Molecule details ›
Chains: E, G, I, K
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DGP*DGP*DCP*DCP*DC)-3' Chains: F, H, J, L
Molecule details ›
Chains: F, H, J, L
Length: 12 nucleotides
Theoretical weight: 3.6 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5CM 4 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 76.198Å b: 111.359Å c: 97.403Å
α: 90° β: 90.53° γ: 90°
R-values:
R R work R free
0.191 0.189 0.231
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

92 review citations

Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Law et al. (2010)
91 more

17 mentions without citation

DNA methylation pathways and their crosstalk with histone methylation.
Du et al. (2015)
16 more