› 5lux

X-ray diffraction
3.23Å resolution

Homeobox transcription factor CDX1 bound to methylated DNA

Released:
DOI: 10.2210/pdb5lux/pdb
PDB entry 5lux coloured by chain, front view.
PDB entry 5lux coloured by chain, side view.
PDB entry 5lux coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J
Science 356 (2017)
PMID: 28473536

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218993 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Homeobox protein CDX-1 Chains: K, L
Molecule details ›
Chains: K, L
Length: 63 amino acids
Theoretical weight: 7.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P47902 (Residues: 153-215; Coverage: 24%)
Gene name: CDX1
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*C)-3') Chain: A
Molecule details ›
Chain: A
Length: 17 nucleotides
Theoretical weight: 5.17 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 18 nucleotides
Theoretical weight: 5.46 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') Chain: F
Molecule details ›
Chain: F
Length: 17 nucleotides
Theoretical weight: 5.27 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3') Chain: E
Molecule details ›
Chain: E
Length: 18 nucleotides
Theoretical weight: 5.6 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: ESRF BEAMLINE ID23-1
Unit cell:
a: 64.65Å b: 45.555Å c: 116.499Å
α: 90° β: 93.79° γ: 90°
R-values:
R R work R free
0.247 0.241 0.3
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

125 review citations

DNA methylation-based biomarkers and the epigenetic clock theory of ageing.
Horvath et al. (2018)
124 more

3 mentions without citation

Detecting and interpreting DNA methylation marks.
Ren et al. (2018)
2 more