2B3Y

Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.str.2005.09.009
  • Primary Citation of Related Structures:  

  • 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 interacti ...

    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.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Data For the Aconitase Form of Human Iron Regulatory Protein 1
      Dupuy, J.,DARNAULT, C.,BRAZZOLOTTO, X.,KUHN, L.C.,MOULIS, J.M.,Volbeda, A.,Fontecilla-Camps, J.C.
      (2005) Acta Crystallogr.,Sect.F 61: 482


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iron-responsive element binding protein 1
A, B
888Homo sapiensMutation(s): 0 
Gene Names: ACO1 (IREB1)
EC: 4.2.1.3
Find proteins for P21399 (Homo sapiens)
Go to Gene View: ACO1
Go to UniProtKB:  P21399
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.910α = 90.00
b = 215.470β = 72.00
c = 64.010γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance