› 1ga5

X-ray diffraction
2.4Å resolution

CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT

Released:
DOI: 10.2210/pdb1ga5/pdb
PDB entry 1ga5 coloured by chain, front view.
PDB entry 1ga5 coloured by chain, side view.
PDB entry 1ga5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
DNA deformability as a recognition feature in the reverb response element.
Sierk ML, Zhao Q, Rastinejad F
Biochemistry 40 12833-43 (2001)
PMID: 11669620

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113860 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Nuclear receptor subfamily 1 group D member 1 Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 94 amino acids
Theoretical weight: 10.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20393 (Residues: 123-216; Coverage: 15%)
Gene names: EAR1, HREV, NR1D1, THRAL
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3' Chains: C, G
Molecule details ›
Chains: C, G
Length: 20 nucleotides
Theoretical weight: 6.14 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3' Chains: D, H
Molecule details ›
Chains: D, H
Length: 20 nucleotides
Theoretical weight: 6.24 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
1 modified residue:
Ligand 5IU 2 x 5IU

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P1
Unit cell:
a: 44.92Å b: 52.02Å c: 78.88Å
α: 85.84° β: 76.61° γ: 74.48°
R-values:
R R work R free
0.236 0.253 0.299
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Origins of specificity in protein-DNA recognition.
Rohs et al. (2010)
8 more

4 mentions without citation

The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins.
Chakraborty et al. (2013)
3 more