2LBD

LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO ALL-TRANS RETINOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid.

Renaud, J.P.Rochel, N.Ruff, M.Vivat, V.Chambon, P.Gronemeyer, H.Moras, D.

(1995) Nature 378: 681-689

  • DOI: 10.1038/378681a0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The 2.0-A crystal structure of the ligand-binding domain (LBD) of the human retinoic acid receptor (RAR)-gamma bound to all-trans retinoic acid reveals the ligand-binding interactions and suggests an electrostatic guidance mechanism. The overall fold ...

    The 2.0-A crystal structure of the ligand-binding domain (LBD) of the human retinoic acid receptor (RAR)-gamma bound to all-trans retinoic acid reveals the ligand-binding interactions and suggests an electrostatic guidance mechanism. The overall fold is similar to that of the human RXR-alpha apo-LBD, except for the carboxy-terminal part which folds back towards the LBD core, contributing to the hydrophobic ligand pocket and 'sealing' its entry site. We propose a 'mouse trap' mechanism whereby a ligand-induced conformational transition repositions the amphipathic alpha-helix of the AF-2 activating domain and forms a transcriptionally active receptor.


    Related Citations: 
    • Crystal Structure of the Ligand-Binding Domain of the Human Nuclear Receptor Rxr-Alpha
      Bourguet, W., Ruff, M., Chambon, P., Gronemeyer, H., Moras, D.
      (1995) Nature 375: 377

    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP/Collège de France, Strasbourg, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RETINOIC ACID RECEPTOR GAMMAA267Homo sapiensMutation(s): 0 
Gene Names: HUMAN RAR GAMMA A CDNA (NUCLEOTIDES 946 - 1683)RARGNR1B3
Find proteins for P13631 (Homo sapiens)
Explore P13631 
Go to UniProtKB:  P13631
NIH Common Fund Data Resources
PHAROS  P13631
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REA
Query on REA

Download CCD File 
A
RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
REAIC50:  1000   nM  BindingDB
REAIC50:  1000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.6α = 90
b = 60.6β = 90
c = 155.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MARXDSdata reduction
MARSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance