6EU9

Crystal structure of Platynereis dumerilii RAR ligand-binding domain in complex with all-trans retinoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation.

Handberg-Thorsager, M.Gutierrez-Mazariegos, J.Arold, S.T.Kumar Nadendla, E.Bertucci, P.Y.Germain, P.Tomancak, P.Pierzchalski, K.Jones, J.W.Albalat, R.Kane, M.A.Bourguet, W.Laudet, V.Arendt, D.Schubert, M.

(2018) Sci Adv 4: eaao1261-eaao1261

  • DOI: 10.1126/sciadv.aao1261
  • Primary Citation of Related Structures:  
    6EU9

  • PubMed Abstract: 
  • Retinoic acid (RA) is an important intercellular signaling molecule in vertebrate development, with a well-established role in the regulation of hox genes during hindbrain patterning and in neurogenesis. However, the evolutionary origin of the RA signaling pathway remains elusive ...

    Retinoic acid (RA) is an important intercellular signaling molecule in vertebrate development, with a well-established role in the regulation of hox genes during hindbrain patterning and in neurogenesis. However, the evolutionary origin of the RA signaling pathway remains elusive. To elucidate the evolution of the RA signaling system, we characterized RA metabolism and signaling in the marine annelid Platynereis dumerilii , a powerful model for evolution, development, and neurobiology. Binding assays and crystal structure analyses show that the annelid retinoic acid receptor (RAR) binds RA and activates transcription just as vertebrate RARs, yet with a different ligand-binding pocket and lower binding affinity, suggesting a permissive rather than instructive role of RA signaling. RAR knockdown and RA treatment of swimming annelid larvae further reveal that the RA signal is locally received in the medial neuroectoderm, where it controls neurogenesis and axon outgrowth, whereas the spatial colinear hox gene expression in the neuroectoderm remains unaffected. These findings suggest that one early role of the new RAR in bilaterian evolution was to control the spatially restricted onset of motor and interneuron differentiation in the developing ventral nerve cord and to indicate that the regulation of hox -controlled anterior-posterior patterning arose only at the base of the chordates, concomitant with a high-affinity RAR needed for the interpretation of a complex RA gradient.


    Organizational Affiliation

    Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230 Villefranche-sur-Mer, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptorA, B, C, D241Platynereis dumeriliiMutation(s): 0 
UniProt
Find proteins for A0A384E144 (Platynereis dumerilii)
Explore A0A384E144 
Go to UniProtKB:  A0A384E144
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REA (Subject of Investigation/LOI)
Query on REA

Download Ideal Coordinates CCD File 
E [auth B], F [auth D]RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.41α = 90
b = 68.15β = 100.75
c = 95.08γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MoRDaphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INBS-05

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations