5ZYS

Structure of Nephrin/MAGI1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural Basis of Highly Specific Interaction between Nephrin and MAGI1 in Slit Diaphragm Assembly and Signaling.

Weng, Z.Shang, Y.Ji, Z.Ye, F.Lin, L.Zhang, R.Zhu, J.

(2018) J Am Soc Nephrol 29: 2362-2371

  • DOI: https://doi.org/10.1681/ASN.2017121275
  • Primary Citation of Related Structures:  
    5ZYS

  • PubMed Abstract: 

    The slit diaphragm is a specialized adhesion junction between opposing podocytes, establishing the final filtration barrier that prevents passage of proteins from the capillary lumen into the urinary space. Nephrin, the key structural and signaling adhesion molecule expressed in the slit diaphragm, contains an evolutionally conserved, atypical PDZ-binding motif (PBM) reported to bind to a variety of proteins in the slit diaphragm. Several mutations in NPHS1 (the gene encoding nephrin) that result in nephrin lacking an intact PBM are associated with glomerular diseases. However, the molecular basis of nephrin-PBM-mediated protein complexes is still unclear.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, Shanghai Science Research Center, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 197Mus musculusMutation(s): 0 
Gene Names: Magi1Baiap1Bap1
UniProt
Find proteins for Q6RHR9 (Mus musculus)
Explore Q6RHR9 
Go to UniProtKB:  Q6RHR9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6RHR9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nephrin10Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.731α = 90
b = 93.731β = 90
c = 93.731γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 2.0: 2019-12-11
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Atomic model, Data collection, Derived calculations, Polymer sequence, Refinement description, Structure summary
  • Version 2.1: 2024-03-27
    Changes: Data collection, Database references