1S1N

SH3 domain of human nephrocystin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a mutation-causing juvenile nephronophthisis.

le Maire, A.Weber, T.Saunier, S.Broutin, I.Antignac, C.Ducruix, A.Dardel, F.

(2005) Proteins 59: 347-355

  • DOI: 10.1002/prot.20344
  • Primary Citation of Related Structures:  
    1S1N

  • PubMed Abstract: 
  • Human nephrocystin is a protein associated with juvenile NPH, an autosomal recessive, inherited kidney disease responsible for chronic renal failure in children. It contains an SH3 domain involved in signaling pathways controlling cell adhesion and cytoskeleton organization ...

    Human nephrocystin is a protein associated with juvenile NPH, an autosomal recessive, inherited kidney disease responsible for chronic renal failure in children. It contains an SH3 domain involved in signaling pathways controlling cell adhesion and cytoskeleton organization. The solution structure of this domain was solved by triple resonance NMR spectroscopy. Within the core, the structure is similar to those previously reported for other SH3 domains but exhibits a number of specific noncanonical features within the polyproline ligand binding site. Some of the key conserved residues are missing, and the N-Src loop exhibits an unusual twisted geometry, which results in a narrowing of the binding groove. This is induced by the replacement of a conserved Asp, Asn, or Glu residue by a Pro at one side of the N-Src loop. A systematic survey of other SH3 domains also containing a Pro at this position reveals that most of them belong to proteins involved in cell adhesion or motility. A variant of this domain, which carries a point mutation causing NPH, was also analyzed. This change, L180P, although it corresponds to a nonconserved and solvent-exposed position, causes a complete loss of the tertiary structure. Similar effects are also observed with the L180A variant. This could be a context-dependent effect resulting from an interaction between neighboring charged side-chains.


    Related Citations: 
    • A novel gene that encodes a protein with a putative src homology 3 domain is a candidate gene for familial juvenile nephronophthisis
      SAUNIER, S., CALADO, J., HEILIG, R., SILBERMANN, F., BENESSY, F., MORIN, G., KONRAD, M., BROYER, M., GUBLER, M.C., WEISSENBACH, J.
      (1997) Hum Mol Genet 6: 21317
    • A novel gene encoding an SH3 domain protein is mutated in nephronophthisis type 1
      HILDEBRANDT, F., OTTO, E., RENSIG, C., NOTHWANG, H.G., VOLLMER, M., ADOLPHS, J., HANUSH, H., BRANDIS, M.
      (1997) Nat Genet 17: 149

    Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques, UMR8015 CNRS, Faculté de Pharmacie, Université Paris 5, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nephrocystin 1A68Homo sapiensMutation(s): 0 
Gene Names: NPHP1NPH1
UniProt & NIH Common Fund Data Resources
Find proteins for O15259 (Homo sapiens)
Explore O15259 
Go to UniProtKB:  O15259
PHAROS:  O15259
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the least restraint violations,structures with the lowest energy 
  • OLDERADO: 1S1N Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references, Derived calculations