3UUM | pdb_00003uum

Crystal Structure of N-terminal first spectrin repeat of utrophin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.268 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

The crystal structures of dystrophin and utrophin spectrin repeats: implications for domain boundaries

Muthu, M.Richardson, K.A.Sutherland-Smith, A.J.

(2012) PLoS One 7: e40066-e40066

  • DOI: https://doi.org/10.1371/journal.pone.0040066
  • Primary Citation Related Structures: 
    3UUL, 3UUM, 3UUN

  • PubMed Abstract: 

    Dystrophin and utrophin link the F-actin cytoskeleton to the cell membrane via an associated glycoprotein complex. This functionality results from their domain organization having an N-terminal actin-binding domain followed by multiple spectrin-repeat domains and then C-terminal protein-binding motifs. Therapeutic strategies to replace defective dystrophin with utrophin in patients with Duchenne muscular dystrophy require full-characterization of both these proteins to assess their degree of structural and functional equivalence. Here the high resolution structures of the first spectrin repeats (N-terminal repeat 1) from both dystrophin and utrophin have been determined by x-ray crystallography. The repeat structures both display a three-helix bundle fold very similar to one another and to homologous domains from spectrin, α-actinin and plectin. The utrophin and dystrophin repeat structures reveal the relationship between the structural domain and the canonical spectrin repeat domain sequence motif, showing the compact structural domain of spectrin repeat one to be extended at the C-terminus relative to its previously defined sequence repeat. These structures explain previous in vitro biochemical studies in which extending dystrophin spectrin repeat domain length leads to increased protein stability. Furthermore we show that the first dystrophin and utrophin spectrin repeats have no affinity for F-actin in the absence of other domains.


  • Organizational Affiliation
    • Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 28.58 kDa 
  • Atom Count: 2,040 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 246 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
utrophin
A, B
123Rattus norvegicusMutation(s): 0 
Gene Names: Utrn
UniProt
Find proteins for O55147 (Rattus norvegicus)
Explore O55147 
Go to UniProtKB:  O55147
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO55147
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.268 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.74α = 90
b = 58.0199β = 90
c = 91.2799γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description