Structure of an orthorhombic crystal form of human cytosolic aconitase (IRP1)

Experimental Data Snapshot

  • Resolution: 2.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 

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Crystal structure of human iron regulatory protein 1 as cytosolic aconitase

Dupuy, J.Volbeda, A.Carpentier, P.Darnault, C.Moulis, J.M.Fontecilla-Camps, J.C.

(2006) Structure 14: 129-139

  • DOI: https://doi.org/10.1016/j.str.2005.09.009
  • Primary Citation of Related Structures:  
    2B3X, 2B3Y

  • PubMed Abstract: 

    Iron regulatory proteins (IRPs) control the translation of proteins involved in iron uptake, storage and utilization by binding to specific noncoding sequences of the corresponding mRNAs known as iron-responsive elements (IREs). This strong interaction assures proper iron homeostasis in animal cells under iron shortage. Conversely, under iron-replete conditions, IRP1 binds a [4Fe-4S] cluster and functions as cytosolic aconitase. Regulation of the balance between the two IRP1 activities is complex, and it does not depend only on iron availability. Here, we report the crystal structure of human IRP1 in its aconitase form. Comparison with known structures of homologous enzymes reveals well-conserved folds and active site environments with significantly different surface shapes and charge distributions. The specific features of human IRP1 allow us to propose a tentative model of an IRP1-IRE complex that agrees with a range of previously obtained data.

  • Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallogenèse des Protéines, Institut de Biologie Structurale JP Ebel, CEA/CNRS/Université Joseph Fourier, 38027 Grenoble Cedex 1, France.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-responsive element binding protein 1888Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P21399 (Homo sapiens)
Explore P21399 
Go to UniProtKB:  P21399
PHAROS:  P21399
GTEx:  ENSG00000122729 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21399
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.352α = 90
b = 103.307β = 90
c = 225.957γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations