4F14

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 

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

  • 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 o ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nebulette
A
64Homo sapiensMutation(s): 0 
Gene Names: NEBL (LNEBL)
Find proteins for O76041 (Homo sapiens)
Go to Gene View: NEBL
Go to UniProtKB:  O76041
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Xin actin-binding repeat-containing protein 2
B
13Homo sapiensMutation(s): 0 
Gene Names: XIRP2 (CMYA3)
Find proteins for A4UGR9 (Homo sapiens)
Go to Gene View: XIRP2
Go to UniProtKB:  A4UGR9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.640α = 90.00
b = 38.420β = 90.00
c = 43.260γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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