6KWZ

Crystal structure of fragmin F3 domain with calcium ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Novel inter-domain Ca2+-binding site in the gelsolin superfamily protein fragmin.

Takeda, S.Fujiwara, I.Sugimoto, Y.Oda, T.Narita, A.Maeda, Y.

(2020) J Muscle Res Cell Motil 41: 153-162

  • DOI: 10.1007/s10974-019-09571-5
  • Primary Citation of Related Structures:  
    6KWZ, 6LJE, 6LJD, 6LJF, 6LJC

  • PubMed Abstract: 
  • Gelsolin superfamily proteins, consisting of multiple domains (usually six), sever actin filaments and cap the barbed ends in a Ca 2+ -dependent manner. Two types of evolutionally conserved Ca 2+ -binding sites have been identif ...

    Gelsolin superfamily proteins, consisting of multiple domains (usually six), sever actin filaments and cap the barbed ends in a Ca 2+ -dependent manner. Two types of evolutionally conserved Ca 2+ -binding sites have been identified in this family; type-1 (between gelsolin and actin) and type-2 (within the gelsolin domain). Fragmin, a member in the slime mold Physarum polycephalum, consists of three domains (F1-F3) that are highly similar to the N-terminal half of mammalian gelsolin (G1-G3). Despite their similarities, the two proteins exhibit a significant difference in the Ca 2+ dependency; F1-F3 absolutely requires Ca 2+ for the filament severing whereas G1-G3 does not. In this study, we examined the strong dependency of fragmin on Ca 2+ using biochemical and structural approaches. Our co-sedimentation assay demonstrated that Ca 2+ significantly enhanced the binding of F2-F3 to actin. We determined the crystal structure of F2-F3 in the presence of Ca 2+ . F2-F3 binds a total of three calcium ions; while two are located in type-2 sites within F2 or F3, the remaining one resides between the F2 long helix and the F3 short helix. The inter-domain Ca 2+ -coordination appears to stabilize F2-F3 in a closely packed configuration. Notably, the F3 long helix exhibits a bent conformation which is different from the straight G3 long helix in the presence of Ca 2+ . Our results provide the first structural evidence for the existence of an unconventional Ca 2+ -binding site in the gelsolin superfamily proteins.


    Organizational Affiliation

    Toyota Physical and Chemical Research Institute, Yokomichi 41-1, Nagakute, Aichi, 480-1192, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-binding protein fragmin PAB98Physarum polycephalumMutation(s): 0 
Find proteins for Q94707 (Physarum polycephalum)
Explore Q94707 
Go to UniProtKB:  Q94707
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.648α = 90
b = 55.076β = 90
c = 69.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-09-09 
  • Released Date: 2020-01-01 
  • Deposition Author(s): Takeda, S.

Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan16K17708
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17K07373

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references