1OVL

Crystal Structure of Nurr1 LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 

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

  • 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, D
271Homo sapiensGene Names: NR4A2 (NOT, NURR1, TINUR)
Find proteins for P43354 (Homo sapiens)
Go to Gene View: NR4A2
Go to UniProtKB:  P43354
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Orphan nuclear receptor NURR1 (MSE 496, 511)
B, C, E, F
271Homo sapiensGene Names: NR4A2 (NOT, NURR1, TINUR)
Find proteins for P43354 (Homo sapiens)
Go to Gene View: NR4A2
Go to UniProtKB:  P43354
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B, D, E, F
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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

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Download CCD File 
A, B, C, D, E, F
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 80.383α = 90.00
b = 80.383β = 90.00
c = 227.370γ = 120.00
Software Package:
Software NamePurpose
CCP4data scaling
SHARPphasing
SCALAdata scaling
MOSFLMdata reduction
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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