› 1skn

X-ray diffraction
2.5Å resolution

THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF

Released:
DOI: 10.2210/pdb1skn/pdb
PDB entry 1skn coloured by chain, front view.
PDB entry 1skn coloured by chain, side view.
PDB entry 1skn coloured by chain, top view.
Source organism: Caenorhabditis elegans
Primary publication:
A new DNA-binding motif in the Skn-1 binding domain-DNA complex.
Rupert PB, Daughdrill GW, Bowerman B, Matthews BW
Nat Struct Biol 5 484-91 (1998)
PMID: 9628487

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114597 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Protein skinhead-1 Chain: P
Molecule details ›
Chain: P
Length: 92 amino acids
Theoretical weight: 11 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P34707 (Residues: 540-623; Coverage: 14%)
Gene names: T19E7.2, skn-1
Sequence domains: bZIP Maf transcription factor
Structure domains: Transcription factor, Skn-1-like, DNA-binding domain
DNA (5'-D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)-3') Chain: A
Molecule details ›
Chain: A
Length: 15 nucleotides
Theoretical weight: 4.53 KDa
Source organism: Caenorhabditis elegans
Expression system: Not provided
DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 15 nucleotides
Theoretical weight: 4.65 KDa
Source organism: Caenorhabditis elegans
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand LDA 1 x LDA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2221
Unit cell:
a: 82.13Å b: 93.39Å c: 53.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.22 0.337
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

11 review citations

SKN-1/Nrf, stress responses, and aging in Caenorhabditis elegans.
Blackwell et al. (2015)
10 more

18 mentions without citation

Frustration in protein-DNA binding influences conformational switching and target search kinetics.
Marcovitz et al. (2011)
17 more