4UMM

The Cryo-EM structure of the palindromic DNA-bound USP-EcR nuclear receptor reveals an asymmetric organization with allosteric domain positioning


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Palindromic DNA-Bound Usp-Ecr Nuclear Receptor Adopts an Asymmetric Organization with Allosteric Domain Positioning.

Maletta, M.Orlov, I.Moras, D.Billas, I.M.L.Klaholz, B.P.

(2014) Nat Commun 5: 4139

  • DOI: 10.1038/ncomms5139
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nuclear receptors (NRs) regulate gene expression through DNA- and ligand-binding and thus represent crucial therapeutic targets. The ultraspiracle protein/ecdysone receptor (USP/EcR) complex binds to half-sites with a one base pair spaced inverted re ...

    Nuclear receptors (NRs) regulate gene expression through DNA- and ligand-binding and thus represent crucial therapeutic targets. The ultraspiracle protein/ecdysone receptor (USP/EcR) complex binds to half-sites with a one base pair spaced inverted repeat (IR1), a palindromic DNA response element (RE) reminiscent of IRs observed for vertebrate steroid hormone receptors. Here we present the cryo electron microscopy structure of the USP/EcR complex bound to an IR1 RE which provides the first description of a full IR-bound NR complex. The structure reveals that even though the DNA is almost symmetric, the complex adopts a highly asymmetric architecture in which the ligand-binding domains (LBDs) are positioned 5' off-centred. Additional interactions of the USP LBD with the 5'-flanking sequence trigger transcription activity as monitored by transfection assays. The comparison with DR-bound NR complexes suggests that DNA is the major allosteric driver in inversely positioning the LBDs, which serve as the main binding-site for transcriptional regulators.


    Organizational Affiliation

    1] Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, 67404 Illkirch, France [2] Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM) U964, 67404 Illkirch, France [4] Université de Strasbourg, 67404 Strasbourg, France.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ECR-USPA78Heliothis virescensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ECDYSONE RECEPTORE87Heliothis virescensMutation(s): 0 
Gene Names: EcRNR1H1
Find proteins for O18473 (Heliothis virescens)
Explore O18473 
Go to UniProtKB:  O18473
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
GENE REGULATION PROTEINF264Heliothis virescensMutation(s): 0 
Find proteins for Q7SIF6 (Heliothis virescens)
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Go to UniProtKB:  Q7SIF6
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ECDYSONE RECEPTORG266Heliothis virescensMutation(s): 0 
Gene Names: EcRNR1H1
Find proteins for O18473 (Heliothis virescens)
Explore O18473 
Go to UniProtKB:  O18473
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP *AP*CP*TP*TP*GP*TP)-3'C20synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*DGP*AP*CP*AP*AP*GP*TP*GP*CP*AP*TP*TP*GP*DAP *AP*CP*CP*CP*TP*T)-3'D20synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPH
Query on EPH

Download CCD File 
F
L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
 Ligand Interaction
P1A
Query on P1A

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G
2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE
C27 H44 O6
PJYYBCXMCWDUAZ-JJJZTNILSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references, Other
  • Version 1.2: 2018-10-03
    Changes: Data collection, Derived calculations