5BVR | pdb_00005bvr

Actin binding domain of alpha-actinin from Schizosaccharomyces pombe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.187 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Characterisation of Schizosaccharomyces pombe alpha-actinin.

Addario, B.Sandblad, L.Persson, K.Backman, L.

(2016) PeerJ 4: e1858-e1858

  • DOI: https://doi.org/10.7717/peerj.1858
  • Primary Citation Related Structures: 
    5BVR

  • PubMed Abstract: 

    The actin cytoskeleton plays a fundamental role in eukaryotic cells. Its reorganization is regulated by a plethora of actin-modulating proteins, such as a-actinin. In higher organisms, α-actinin is characterized by the presence of three distinct structural domains: an N-terminal actin-binding domain and a C-terminal region with EF-hand motif separated by a central rod domain with four spectrin repeats. Sequence analysis has revealed that the central rod domain of α-actinin from the fission yeast Schizosaccharomyces pombe consists of only two spectrin repeats. To obtain a firmer understanding of the structure and function of this unconventional α-actinin, we have cloned and characterized each structural domain. Our results show that this a-actinin isoform is capable of forming dimers and that the rod domain is required for this. However, its actin-binding and cross-linking activity appears less efficient compared to conventional α-actinins. The solved crystal structure of the actin-binding domain indicates that the closed state is stabilised by hydrogen bonds and a salt bridge not present in other α-actinins, which may reduce the affinity for actin.


  • Organizational Affiliation
    • Cell Biology Laboratory, School of Biochemistry and Cell Biology, BioScience Institute, University College Cork , Cork , Ireland.

Macromolecule Content 

  • Total Structure Weight: 27.49 kDa 
  • Atom Count: 2,170 
  • Modeled Residue Count: 229 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-actinin-like protein 1236Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ain1SPAC15A10.08
UniProt
Find proteins for O13728 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13728 
Go to UniProtKB:  O13728
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13728
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.537α = 90
b = 79.468β = 90
c = 91.933γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Car trygger foundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description