5UAN

Crystal structure of multi-domain RAR-beta-RXR-alpha heterodimer on DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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Literature

The quaternary architecture of RAR beta-RXR alpha heterodimer facilitates domain-domain signal transmission.

Chandra, V., Wu, D., Li, S., Potluri, N., Kim, Y., Rastinejad, F.

(2017) Nat Commun 8: 868-868

  • DOI: 10.1038/s41467-017-00981-y
  • Primary Citation of Related Structures:  
    5UAN

  • PubMed Abstract: 

    • Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor β-retinoic X receptor α (RARβ-RXRα) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies ...

    Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor β-retinoic X receptor α (RARβ-RXRα) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RARβ ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within their quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its heterodimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.Nuclear receptors (NR) are multidomain proteins, which makes their crystallization challenging. Here the authors present the crystal structure of the retinoic acid receptor β-retinoic X receptor α (RARβ-RXRα) heterodimer bound to DNA, ligands and coactivator peptides, which shows that NR quaternary architectures are variable.

    Organizational Affiliation: 

    Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, 32827, USA. frastinejad@sbpdiscovery.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA365Homo sapiensMutation(s): 0 
Gene Names: RXRA, NR2B1
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Find proteins for P19793 (Homo sapiens)
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Go to UniProtKB:  P19793
PHAROS:  P19793
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UniProt GroupP19793
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor betaB397Homo sapiensMutation(s): 0 
Gene Names: RARB, HAP, NR1B2
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Find proteins for P10826 (Homo sapiens)
Explore P10826 
Go to UniProtKB:  P10826
PHAROS:  P10826
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UniProt GroupP10826
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2C, D10Homo sapiensMutation(s): 0 
Gene Names: NCOA2, BHLHE75, SRC2, TIF2
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Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
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UniProt GroupQ15596
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*GP*C)-3')E17Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')F17Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REA
Query on REA
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L [auth B]RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N		 Ligand Interaction
9CR
Query on 9CR
Download Ideal Coordinates CCD File 
I [auth A](9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth B],
K [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9CR BindingDB:  5UAN Ki: min: 0.5, max: 583 (nM) from 11 assay(s)
Kd: min: 0.8, max: 1810 (nM) from 24 assay(s)
IC50: min: 7, max: 82 (nM) from 7 assay(s)
EC50: min: 1.5, max: 316 (nM) from 32 assay(s)
REA BindingDB:  5UAN IC50: min: 1000, max: 5.00e+4 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.47α = 90
b = 77.403β = 90.37
c = 112.113γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references