4F14

Structure of the SH3 domain of human nebulette in complex with a peptide of XIRP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of Xin-repeat proteins as novel ligands of the SH3 domains of nebulin and nebulette and analysis of their interaction during myofibril formation and remodeling.

Eulitz, S.Sauer, F.Pelissier, M.C.Boisguerin, P.Molt, S.Schuld, J.Orfanos, Z.Kley, R.A.Volkmer, R.Wilmanns, M.Kirfel, G.van der Ven, P.F.Furst, D.O.

(2013) Mol Biol Cell 24: 3215-3226

  • DOI: 10.1091/mbc.E13-04-0202
  • Primary Citation of Related Structures:  
    4F14

  • PubMed Abstract: 
  • The Xin actin-binding repeat-containing proteins Xin and XIRP2 are exclusively expressed in striated muscle cells, where they are believed to play an important role in development. In adult muscle, both proteins are concentrated at attachment sites of myofibrils to the membrane ...

    The Xin actin-binding repeat-containing proteins Xin and XIRP2 are exclusively expressed in striated muscle cells, where they are believed to play an important role in development. In adult muscle, both proteins are concentrated at attachment sites of myofibrils to the membrane. In contrast, during development they are localized to immature myofibrils together with their binding partner, filamin C, indicating an involvement of both proteins in myofibril assembly. We identify the SH3 domains of nebulin and nebulette as novel ligands of proline-rich regions of Xin and XIRP2. Precise binding motifs are mapped and shown to bind both SH3 domains with micromolar affinity. Cocrystallization of the nebulette SH3 domain with the interacting XIRP2 peptide PPPTLPKPKLPKH reveals selective interactions that conform to class II SH3 domain-binding peptides. Bimolecular fluorescence complementation experiments in cultured muscle cells indicate a temporally restricted interaction of Xin-repeat proteins with nebulin/nebulette during early stages of myofibril development that is lost upon further maturation. In mature myofibrils, this interaction is limited to longitudinally oriented structures associated with myofibril development and remodeling. These data provide new insights into the role of Xin actin-binding repeat-containing proteins (together with their interaction partners) in myofibril assembly and after muscle damage.


    Organizational Affiliation

    Institute for Cell Biology, University of Bonn, D-53121 Bonn, Germany European Molecular Biology Laboratory-Hamburg/Deutsches Elektronen-Synchrotron, D-22603 Hamburg, Germany Department of Medicinal Immunology, Charité-University Medicine Berlin, D-13353 Berlin, Germany Department of Neurology, Neuromuscular Center Ruhrgebiet, University Hospital Bergmannsheil, Ruhr-University Bochum, D-44789 Bochum, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NebuletteA64Homo sapiensMutation(s): 0 
Gene Names: NEBLLNEBL
UniProt & NIH Common Fund Data Resources
Find proteins for O76041 (Homo sapiens)
Explore O76041 
Go to UniProtKB:  O76041
PHAROS:  O76041
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Xin actin-binding repeat-containing protein 2B13Homo sapiensMutation(s): 0 
Gene Names: XIRP2CMYA3
UniProt & NIH Common Fund Data Resources
Find proteins for A4UGR9 (Homo sapiens)
Explore A4UGR9 
Go to UniProtKB:  A4UGR9
PHAROS:  A4UGR9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.64α = 90
b = 38.42β = 90
c = 43.26γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description