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: RXRANR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
GTEx:  ENSG00000186350 
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UniProt GroupP19793
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor betaB397Homo sapiensMutation(s): 0 
Gene Names: RARBHAPNR1B2
UniProt & NIH Common Fund Data Resources
Find proteins for P10826 (Homo sapiens)
Explore P10826 
Go to UniProtKB:  P10826
PHAROS:  P10826
GTEx:  ENSG00000077092 
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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: NCOA2BHLHE75SRC2TIF2
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Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
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UniProt GroupQ15596
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  • Reference Sequence

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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')E 17Homo 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')F 17Homo sapiens
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REA
Query on REA

Download Ideal Coordinates CCD File 
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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Ligand Structure Quality Assessment 



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