1OVL

Crystal Structure of Nurr1 LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and Function of Nurr1 identifies a Class of Ligand-Independent Nuclear Receptors

Wang, Z.Benoit, G.Liu, J.Prasad, S.Aarnisalo, P.Liu, X.Xu, H.Walker, N.Perlmann, T.

(2003) Nature 423: 555-560

  • DOI: 10.1038/nature01645
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Members of the nuclear receptor (NR) superfamily of transcription factors modulate gene transcription in response to small lipophilic molecules. Transcriptional activity is regulated by ligands binding to the carboxy-terminal ligand-binding domains ( ...

    Members of the nuclear receptor (NR) superfamily of transcription factors modulate gene transcription in response to small lipophilic molecules. Transcriptional activity is regulated by ligands binding to the carboxy-terminal ligand-binding domains (LBDs) of cognate NRs. A subgroup of NRs referred to as 'orphan receptors' lack identified ligands, however, raising issues about the function of their LBDs. Here we report the crystal structure of the LBD of the orphan receptor Nurr1 at 2.2 A resolution. The Nurr1 LBD adopts a canonical protein fold resembling that of agonist-bound, transcriptionally active LBDs in NRs, but the structure has two distinctive features. First, the Nurr1 LBD contains no cavity as a result of the tight packing of side chains from several bulky hydrophobic residues in the region normally occupied by ligands. Second, Nurr1 lacks a 'classical' binding site for coactivators. Despite these differences, the Nurr1 LBD can be regulated in mammalian cells. Notably, transcriptional activity is correlated with the Nurr1 LBD adopting a more stable conformation. Our findings highlight a unique structural class of NRs and define a model for ligand-independent NR function.


    Organizational Affiliation

    Department of Structural Biology, Tularik Inc., 1120 Veterans Blvd., South San Francisco, California 94080, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orphan nuclear receptor NURR1 (MSE 414, 496, 511)A, D271Homo sapiensMutation(s): 2 
Gene Names: NR4A2 OR NURR1 OR TINUR OR NOTNR4A2NOTNURR1TINUR
Find proteins for P43354 (Homo sapiens)
Explore P43354 
Go to UniProtKB:  P43354
NIH Common Fund Data Resources
PHAROS  P43354
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Orphan nuclear receptor NURR1 (MSE 496, 511)B, C, E, F271Homo sapiensMutation(s): 3 
Gene Names: NR4A2 OR NURR1 OR TINUR OR NOTNR4A2NOTNURR1TINUR
Find proteins for P43354 (Homo sapiens)
Explore P43354 
Go to UniProtKB:  P43354
NIH Common Fund Data Resources
PHAROS  P43354
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download CCD File 
B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
BR
Query on BR

Download CCD File 
A, B, C, D, E, F
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

Download CCD File 
A, B, D, E, F
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.231 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.383α = 90
b = 80.383β = 90
c = 227.37γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNXrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance