› 5hod

X-ray diffraction
2.68Å resolution

Structure of LHX4 transcription factor complexed with DNA

Released:
DOI: 10.2210/pdb5hod/pdb
PDB entry 5hod coloured by chain, front view.
PDB entry 5hod coloured by chain, side view.
PDB entry 5hod 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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118747 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
LIM/homeobox protein Lhx4 Chains: A, D
Molecule details ›
Chains: A, D
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q969G2 (Residues: 156-216; Coverage: 16%)
Gene name: LHX4
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
DNA (5'-D(P*AP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*GP*TP*AP*AP*TP*TP*AP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 20 nucleotides
Theoretical weight: 6.16 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*CP*TP*AP*AP*TP*TP*AP*CP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 20 nucleotides
Theoretical weight: 6.11 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2221
Unit cell:
a: 40.768Å b: 68.442Å c: 200.464Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.233 0.261
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

4 mentions without citation

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