› 6gcd

X-ray diffraction
1.8Å resolution

DNA binding domain of restriction endonuclease McrBC in complex with 5-hydroxymethylcytosine DNA

Released:
DOI: 10.2210/pdb6gcd/pdb
PDB entry 6gcd coloured by chain, front view.
PDB entry 6gcd coloured by chain, side view.
PDB entry 6gcd coloured by chain, top view.
Source organisms:
Primary publication:
Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC.
Zagorskaitė E, Manakova E, Sasnauskas G
FEBS Lett 592 3335-3345 (2018)
PMID: 30194838

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119941 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type IV methyl-directed restriction enzyme EcoKMcrB subunit Chains: A, B
Molecule details ›
Chains: A, B
Length: 170 amino acids
Theoretical weight: 19.74 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli str. K-12 substr. DH10B
UniProt:
  • Canonical: P15005 (Residues: 1-161; Coverage: 35%)
Gene names: JW5871, b4346, mcrB, rglB
Sequence domains: MrcB-like, N-terminal domain
Structure domains: Metal Transport, Frataxin; Chain A
DNA (5'-D(*GP*AP*GP*AP*(5HC)P*CP*GP*GP*TP*AP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.74 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*AP*(5HC)P*CP*GP*GP*TP*CP*TP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
2 modified residues:
Ligand CME 2 x CME
Ligand 5HC 2 x 5HC

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU R-AXIS IV
Spacegroup: P212121
Unit cell:
a: 36.071Å b: 68.934Å c: 143.708Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.166 0.214
Expression systems:
  • Escherichia coli str. K-12 substr. DH10B
  • Not provided

Quick links

Citations

6 citation in other articles

Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA.
Woodcock et al. (2020)
5 more