Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.55 kDa 
• Atom Count: 1826 
• Modelled Residue Count: 224 
• Deposited Residue Count: 259 
• Unique protein chains: 2

1XB7

X-ray structure of ERRalpha LBD in complex with a PGC-1alpha peptide at 2.5A resolution

• PDB DOI: 10.2210/pdb1XB7/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2004-08-30 Released: 2004-09-14 
• Deposition Author(s): Kallen, J., Schlaeppi, J.M., Bitsch, F., Filipuzzi, I., Schilb, A., Riou, V., Graham, A., Strauss, A., Geiser, M., Fournier, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.247 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

Literature

Evidence for Ligand-independent Transcriptional Activation of the Human Estrogen-related Receptor {alpha} (ERR{alpha}): CRYSTAL STRUCTURE OF ERR{alpha} LIGAND BINDING DOMAIN IN COMPLEX WITH PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR COACTIVATOR-1{alpha}

Kallen, J., Schlaeppi, J.M., Bitsch, F., Filipuzzi, I., Schilb, A., Riou, V., Graham, A., Strauss, A., Geiser, M., Fournier, B.

(2004) J Biol Chem 279: 49330-49337

• PubMed: 15337744 
• DOI: 10.1074/jbc.M407999200
• Primary Citation of Related Structures:  
  1XB7


• PubMed Abstract: 
  

The crystal structure of the ligand binding domain (LBD) of the estrogen-related receptor alpha (ERRalpha, NR3B1) complexed with a coactivator peptide from peroxisome proliferator-activated receptor coactivator-1alpha (PGC-1alpha) reveals a transcriptionally active conformation in the absence of a ligand. This is the first x-ray structure of ERRalpha LBD, solved to a resolution of 2.5 A, and the first structure of a PGC-1alpha complex. The putative ligand binding pocket (LBP) of ERRalpha is almost completely occupied by side chains, in particular with the bulky side chain of Phe328 (corresponding to Ala272 in ERRgamma and Ala350 in estrogen receptor alpha). Therefore, a ligand of a size equivalent to more than approximately 4 carbon atoms could only bind in the LBP, if ERRalpha would undergo a major conformational change (in particular the ligand would displace H12 from its agonist position). The x-ray structure thus provides strong evidence for ligand-independent transcriptional activation by ERRalpha. The interactions of PGC-1alpha with ERRalpha also reveal for the first time the atomic details of how a coactivator peptide containing an inverted LXXLL motif (namely a LLXYL motif) binds to a LBD. In addition, we show that a PGC-1alpha peptide containing this nuclear box motif from the L3 site binds ERRalpha LBD with a higher affinity than a peptide containing a steroid receptor coactivator-1 motif and that the affinity is further enhanced when all three leucine-rich regions of PGC-1alpha are present.

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Organizational Affiliation: 

Protein Structure Unit, Novartis Institutes for Biomedical Research, Basel, Switzerland. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid hormone receptor ERR1	A	247	Homo sapiens	Mutation(s): 0  Gene Names: ESRRA, ERR1, ESRL1, NR3B1
UniProt & NIH Common Fund Data Resources
Find proteins for P11474 (Homo sapiens) Explore P11474  Go to UniProtKB:  P11474
PHAROS:  P11474

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator activated receptor gamma coactivator 1 alpha	B [auth P]	12	N/A	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2  Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth P]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.247 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.999	α = 90
b = 109.999	β = 90
c = 104.671	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-30 
• Released Date: 2004-09-14 
Deposition Author(s): Kallen, J., Schlaeppi, J.M., Bitsch, F., Filipuzzi, I., Schilb, A., Riou, V., Graham, A., Strauss, A., Geiser, M., Fournier, B.

Revision History  

• Version 1.0: 2004-09-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations