6FBB

Crystal structure of 14-3-3 sigma in complex with wild-type Shroom3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Characterization of Coding/Noncoding Variants forSHROOM3in Patients with CKD.

Prokop, J.W.Yeo, N.C.Ottmann, C.Chhetri, S.B.Florus, K.L.Ross, E.J.Sosonkina, N.Link, B.A.Freedman, B.I.Coppola, C.J.McDermott-Roe, C.Leysen, S.Milroy, L.G.Meijer, F.A.Geurts, A.M.Rauscher, F.J.Ramaker, R.Flister, M.J.Jacob, H.J.Mendenhall, E.M.Lazar, J.

(2018) J Am Soc Nephrol 29: 1525-1535

  • DOI: https://doi.org/10.1681/ASN.2017080856
  • Primary Citation of Related Structures:  
    6FBB, 6FCP

  • PubMed Abstract: 

    Background Interpreting genetic variants is one of the greatest challenges impeding analysis of rapidly increasing volumes of genomic data from patients. For example, SHROOM3 is an associated risk gene for CKD, yet causative mechanism(s) of SHROOM3 allele(s) are unknown. Methods We used our analytic pipeline that integrates genetic, computational, biochemical, CRISPR/Cas9 editing, molecular, and physiologic data to characterize coding and noncoding variants to study the human SHROOM3 risk locus for CKD. Results We identified a novel SHROOM3 transcriptional start site, which results in a shorter isoform lacking the PDZ domain and is regulated by a common noncoding sequence variant associated with CKD (rs17319721, allele frequency: 0.35). This variant disrupted allele binding to the transcription factor TCF7L2 in podocyte cell nuclear extracts and altered transcription levels of SHROOM3 in cultured cells, potentially through the loss of repressive looping between rs17319721 and the novel start site. Although common variant mechanisms are of high utility, sequencing is beginning to identify rare variants involved in disease; therefore, we used our biophysical tools to analyze an average of 112,849 individual human genome sequences for rare SHROOM3 missense variants, revealing 35 high-effect variants. The high-effect alleles include a coding variant (P1244L) previously associated with CKD ( P =0.01, odds ratio=7.95; 95% CI, 1.53 to 41.46) that we find to be present in East Asian individuals at an allele frequency of 0.0027. We determined that P1244L attenuates the interaction of SHROOM3 with 14-3-3, suggesting alterations to the Hippo pathway, a known mediator of CKD. Conclusions These data demonstrate multiple new SHROOM3 -dependent genetic/molecular mechanisms that likely affect CKD.


  • Organizational Affiliation

    HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; jprokop54@gmail.com jlazar@hudsonalpha.org.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein sigma236Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
GTEx:  ENSG00000175793 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31947
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Shroom3B [auth P]5Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF72 (Homo sapiens)
Explore Q8TF72 
Go to UniProtKB:  Q8TF72
PHAROS:  Q8TF72
GTEx:  ENSG00000138771 
Entity Groups  
UniProt GroupQ8TF72
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.528α = 90
b = 112.241β = 90
c = 62.725γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-09
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary