4WIQ | pdb_00004wiq

The structure of Murine alpha-Dystroglycan T190M mutant N-terminal domain.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.163 (Depositor), 0.168 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4WIQ

This is version 1.2 of the entry. See complete history

Literature

The Structure of the T190M Mutant of Murine alpha-Dystroglycan at High Resolution: Insight into the Molecular Basis of a Primary Dystroglycanopathy.

Bozzi, M.Cassetta, A.Covaceuszach, S.Bigotti, M.G.Bannister, S.Hubner, W.Sciandra, F.Lamba, D.Brancaccio, A.

(2015) PLoS One 10: e0124277-e0124277

  • DOI: https://doi.org/10.1371/journal.pone.0124277
  • Primary Citation Related Structures: 
    4WIQ

  • PubMed Abstract: 

    The severe dystroglycanopathy known as a form of limb-girdle muscular dystrophy (LGMD2P) is an autosomal recessive disease caused by the point mutation T192M in α-dystroglycan. Functional expression analysis in vitro and in vivo indicated that the mutation was responsible for a decrease in posttranslational glycosylation of dystroglycan, eventually interfering with its extracellular-matrix receptor function and laminin binding in skeletal muscle and brain. The X-ray crystal structure of the missense variant T190M of the murine N-terminal domain of α-dystroglycan (50-313) has been determined, and showed an overall topology (Ig-like domain followed by a basket-shaped domain reminiscent of the small subunit ribosomal protein S6) very similar to that of the wild-type structure. The crystallographic analysis revealed a change of the conformation assumed by the highly flexible loop encompassing residues 159-180. Moreover, a solvent shell reorganization around Met190 affects the interaction between the B1-B5 anti-parallel strands forming part of the floor of the basket-shaped domain, with likely repercussions on the folding stability of the protein domain(s) and on the overall molecular flexibility. Chemical denaturation and limited proteolysis experiments point to a decreased stability of the T190M variant with respect to its wild-type counterpart. This mutation may render the entire L-shaped protein architecture less flexible. The overall reduced flexibility and stability may affect the functional properties of α-dystroglycan via negatively influencing its binding behavior to factors needed for dystroglycan maturation, and may lay the molecular basis of the T190M-driven primary dystroglycanopathy.


  • Organizational Affiliation
    • Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma 00168, Italy.

Macromolecule Content 

  • Total Structure Weight: 28.67 kDa 
  • Atom Count: 1,994 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 264 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dystroglycan264Mus musculusMutation(s): 2 
Gene Names: Dag1Dag-1
UniProt
Find proteins for Q62165 (Mus musculus)
Explore Q62165 
Go to UniProtKB:  Q62165
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62165
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.163 (Depositor), 0.168 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.879α = 90
b = 71.879β = 90
c = 144.296γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary