4NUF

Crystal Structure of SHP/EID1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report



Literature

Structural insights into gene repression by the orphan nuclear receptor SHP.

Zhi, X.Zhou, X.E.He, Y.Zechner, C.Suino-Powell, K.M.Kliewer, S.A.Melcher, K.Mangelsdorf, D.J.Xu, H.E.

(2014) Proc Natl Acad Sci U S A 111: 839-844

  • DOI: 10.1073/pnas.1322827111
  • Primary Citation of Related Structures:  
    4NUF

  • PubMed Abstract: 
  • Small heterodimer partner (SHP) is an orphan nuclear receptor that functions as a transcriptional repressor to regulate bile acid and cholesterol homeostasis. Although the precise mechanism whereby SHP represses transcription is not known, E1A-like inhibitor of differentiation (EID1) was isolated as a SHP-interacting protein and implicated in SHP repression ...

    Small heterodimer partner (SHP) is an orphan nuclear receptor that functions as a transcriptional repressor to regulate bile acid and cholesterol homeostasis. Although the precise mechanism whereby SHP represses transcription is not known, E1A-like inhibitor of differentiation (EID1) was isolated as a SHP-interacting protein and implicated in SHP repression. Here we present the crystal structure of SHP in complex with EID1, which reveals an unexpected EID1-binding site on SHP. Unlike the classical cofactor-binding site near the C-terminal helix H12, the EID1-binding site is located at the N terminus of the receptor, where EID1 mimics helix H1 of the nuclear receptor ligand-binding domain. The residues composing the SHP-EID1 interface are highly conserved. Their mutation diminishes SHP-EID1 interactions and affects SHP repressor activity. Together, these results provide important structural insights into SHP cofactor recruitment and repressor function and reveal a conserved protein interface that is likely to have broad implications for transcriptional repression by orphan nuclear receptors.


    Organizational Affiliation

    Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose ABC transporter periplasmic protein, Nuclear receptor subfamily 0 group B member 2 chimeric constructA580Escherichia coli O104:H4 str. 2009EL-2071Mus musculus
This entity is chimeric
Mutation(s): 5 
Gene Names: malEmalE O3O_01660Nr0b2Shp
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Go to UniProtKB:  Q62227
Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EID1 peptideP16N/AMutation(s): 0 
Find proteins for Q9DCR4 (Mus musculus)
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Go to UniProtKB:  Q9DCR4
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2 N/A
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Balpha-maltoseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.388α = 90
b = 105.148β = 90
c = 136.277γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary