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1A6Y|pdb_00001a6y
REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX
- PDB DOI: https://doi.org/10.2210/pdb1A6Y/pdb
- NAKB: 1A6Y
- Classification: TRANSCRIPTION/DNA
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 1998-03-04 Released: 1998-10-21
- Deposition Author(s): Zhao, Q.,Khorasanizadeh, S.,Rastinejad, F.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.288 (Depositor), 0.260 (DCC)
- R-Value Work: 0.192 (Depositor), 0.210 (DCC)
Starting Model:experimental
View more details
wwPDB Validation 3D Report Full Report
Download MendeleyStructural elements of an orphan nuclear receptor-DNA complex.
Zhao, Q., Khorasanizadeh, S., Miyoshi, Y., Lazar, M.A., Rastinejad, F.(1998) Mol Cell 1: 849-861
- PubMed: 9660968 Search on PubMed
- DOI: https://doi.org/10.1016/s1097-2765(00)80084-2
- Primary Citation of Related Structures:
1A6Y - PubMed Abstract:
The nuclear hormone receptors form the largest known family of transcription factors. The current notion of receptor DNA discrimination, based solely on one major type of hexameric half-site and a highly conserved 66-residue core DNA-binding domain (DBD), does not adequately describe how more than 150 nonsteroid receptors differentiate among response elements. Here, we describe the 2.3 A crystal structure of the DNA-binding region of the orphan receptor RevErb arranged as a tandem homodimer on its optimal response element. The structure reveals the presence of a second major protein-DNA interface adjacent to the classical one involving the half-sites. A sequence comparison of orphan receptors suggests that unique minor-groove interactions involving the receptor hinge regions impart the necessary DNA and dimerization specificity.
- Department of Pharmacology, School of Medicine, University of Virginia, Charlottesville 22908, USA.
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (ZN)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Homo 2-mer - A2
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 34.45 kDa
- Atom Count: 2,334
- Modeled Residue Count: 202
- Deposited Residue Count: 228
- Unique protein chains: 1
- Unique nucleic acid chains: 2
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ORPHAN NUCLEAR RECEPTOR NR1D1 | C [auth A], D [auth B] | 94 | Homo sapiens | Mutation(s): 0 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P20393 (Homo sapiens) Explore P20393 Go to UniProtKB: P20393 | |||||
PHAROS: P20393 GTEx: ENSG00000126368 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P20393 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*(5IT)P*AP*GP*GP*TP*CP*AP*G)-3') | A [auth C] | 20 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*G)-3') | B [auth D] | 20 | N/A |  | |
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN Download Ideal Coordinates CCD File
| E [auth A], F [auth A], G [auth B], H [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.288 (Depositor), 0.260 (DCC)
- R-Value Work: 0.192 (Depositor), 0.210 (DCC)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 38.67 | α = 75.16 |
| b = 45.69 | β = 80.64 |
| c = 47.95 | γ = 85.58 |
| Software Name | Purpose |
|---|---|
| AMoRE | phasing |
| X-PLOR | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Deposition Data
- Released Date: 1998-10-21 Deposition Author(s): Zhao, Q.,Khorasanizadeh, S.,Rastinejad, F.
Revision History (Full details and data files)
- Version 1.0: 1998-10-21
Type: Initial release - Version 1.1: 2008-05-22
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2023-08-02
Changes: Data collection, Database references, Derived calculations, Refinement description
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