Human microglia-specific protein Iba1

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

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This is version 1.2 of the entry. See complete history


X-ray Structures of the Microglia/Macrophage-specific Protein Iba1 from Human and Mouse Demonstrate Novel Molecular Conformation Change Induced by Calcium binding

Yamada, M.Ohsawa, K.Imai, Y.Kohsaka, S.Kamitori, S.

(2006) J Mol Biol 364: 449-457

  • DOI: https://doi.org/10.1016/j.jmb.2006.09.027
  • Primary Citation of Related Structures:  
    1WY9, 2D58

  • PubMed Abstract: 

    The ionized calcium-binding adaptor molecule 1 (Iba1) with 147 amino acid residues has been identified as a calcium-binding protein, expressed specifically in microglia/macrophages, and is expected to be a key factor in membrane ruffling, which is a typical feature of activated microglia. We have determined the crystal structure of human Iba1 in a Ca(2+)-free form and mouse Iba1 in a Ca(2+)-bound form, to a resolution of 1.9 A and 2.1 A, respectively. X-ray structures of Iba1 revealed a compact, single-domain protein with two EF-hand motifs, showing similarity in overall topology to partial structures of the classical EF-hand proteins troponin C and calmodulin. In mouse Iba1, the second EF-hand contains a bound Ca(2+), but the first EF-hand does not, which is often the case in S100 proteins, suggesting that Iba1 has S100 protein-like EF-hands. The molecular conformational change induced by Ca(2+)-binding of Iba1 is different from that found in the classical EF-hand proteins and/or S100 proteins, which demonstrates that Iba1 has an unique molecular switching mechanism dependent on Ca(2+)-binding, to interact with target molecules.

  • Organizational Affiliation

    Information Technology Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allograft inflammatory factor 1107Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P55008 (Homo sapiens)
Explore P55008 
Go to UniProtKB:  P55008
GTEx:  ENSG00000204472 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55008
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.748α = 90
b = 36.617β = 99.71
c = 44.024γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2006-10-10 
  • Deposition Author(s): Kamitori, S.

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance