2LBD

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

• PDB DOI: https://doi.org/10.2210/pdb2LBD/pdb

• Classification: NUCLEAR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1997-08-19 Released: 1997-11-12 
• Deposition Author(s): Renaud, J.-P., Rochel, N., Ruff, M., Moras, D., Structural Proteomics in Europe (SPINE)

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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 

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

• PubMed: 7501014 
• DOI: https://doi.org/10.1038/378681a0
• Primary Citation of Related Structures:  
  2LBD


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.49 kDa 
• Atom Count: 2,020 
• Modelled Residue Count: 238 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RETINOIC ACID RECEPTOR GAMMA	A	267	Homo sapiens	Mutation(s): 0  Gene Names: HUMAN RAR GAMMA A CDNA (NUCLEOTIDES 946 - 1683)
UniProt & NIH Common Fund Data Resources
Find proteins for P13631 (Homo sapiens) Explore P13631  Go to UniProtKB:  P13631
PHAROS:  P13631 GTEx:  ENSG00000172819

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
REA	B [auth A]	RETINOIC ACID C20 H28 O2 SHGAZHPCJJPHSC-YCNIQYBTSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
REA	BindingDB:  2LBD	IC50: min: 1000, max: 1000 (nM) from 2 assay(s)

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 = 60.6	α = 90
b = 60.6	β = 90
c = 155.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MARXDS	data reduction
MARSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-12 
Deposition Author(s): Renaud, J.-P., Rochel, N., Ruff, M., Moras, D., Structural Proteomics in Europe (SPINE)

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
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Other