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

Experimental Data Snapshot

  • Resolution: 1.3 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history


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: 10.1681/ASN.2017080856
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <b>Background </b> Interpreting genetic variants is one of the greatest challenges impeding analysis of rapidly increasing volumes of genomic data from patients. For example, <i>SHROOM3 </i> is an associated risk gene for CKD, yet causative mechani ...

    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

    Gene Expression & Regulation Program, Wistar Institute, Philadelphia, Pennsylvania.,Department of Chemistry, University of Duisburg-Essen, Essen, Germany.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Department of Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee.,Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina; and.,Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; jprokop54@gmail.com jlazar@hudsonalpha.org.,Department of Cell Biology, Neurobiology and Anatomy and.,Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan.,Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama.,Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein sigma
236Homo sapiensMutation(s): 0 
Gene Names: SFN (HME1)
Find proteins for P31947 (Homo sapiens)
Go to Gene View: SFN
Go to UniProtKB:  P31947
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5Homo sapiensMutation(s): 0 
Gene Names: SHROOM3 (KIAA1481, SHRML)
Find proteins for Q8TF72 (Homo sapiens)
Go to Gene View: SHROOM3
Go to UniProtKB:  Q8TF72
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on CL

Download SDF File 
Download CCD File 
 Ligand Interaction
Query on MG

Download SDF File 
Download CCD File 
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
Query on SEP
Experimental Data & Validation

Experimental Data

  • Resolution: 1.3 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.154 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.528α = 90.00
b = 112.241β = 90.00
c = 62.725γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Database references
  • Version 1.2: 2018-05-09
    Type: Data collection, Database references, Source and taxonomy