Crystal structure of the calponin homology domain of IQGAP1

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 

Starting Model: experimental
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The IQGAP1 N-Terminus Forms Dimers, and the Dimer Interface Is Required for Binding F-Actin and Calcium-Bound Calmodulin.

Liu, J.Kurella, V.B.LeCour Jr., L.Vanagunas, T.Worthylake, D.K.

(2016) Biochemistry 55: 6433-6444

  • DOI: https://doi.org/10.1021/acs.biochem.6b00745
  • Primary Citation of Related Structures:  
    3I6X, 5L0O

  • PubMed Abstract: 

    IQGAP1 is a multidomain scaffold protein involved in many cellular processes. We have determined the crystal structure of an N-terminal fragment spanning residues 1-191 (CHDF hereafter) that contains the entire calponin homology domain. The structure of the CHDF is very similar to those of other type 3 calponin homology domains like those from calponin, Vav, and the yeast IQGAP1 ortholog Rng2. However, in the crystal, two CHDF molecules form a "head-to-head" or parallel dimer through mostly hydrophobic interactions. Binding experiments indicate that the CHDF binds to both F-actin and Ca 2+ /calmodulin, but binding is mutually exclusive. On the basis of the structure, two dimer interface substitutions were introduced. While CHDFL157D disrupts the dimer in gel filtration experiments, oxidized CHDFK161C stabilizes the dimer. These results imply that the CHDF forms the same dimer in solution that is seen in the crystal structure. The disulfide-stabilized dimer displays a reduced level of F-actin binding in sedimentation assays and shows no binding to Ca 2+ /calmodulin in isothermal titration calorimetry (ITC) experiments, indicating that interface residues are utilized for both binding events. The Calmodulin Target Database predicts that residues 93 KK 94 are important for CaM binding, and indeed, the 93 EE 94 double mutation displays a reduced level of binding to Ca 2+ /calmodulin in ITC experiments. Our results indicate that the CHDF dimer interface is used for both F-actin and Ca 2+ /calmodulin binding, and the 93 KK 94 pair, near the interface, is also used for Ca 2+ /calmodulin binding. These results are also consistent with full-length IQGAP1 forming a parallel homodimer.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center-New Orleans , 1901 Perdido Street, New Orleans, Louisiana 70112, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras GTPase-activating-like protein IQGAP1
A, B, C, D
193Homo sapiensMutation(s): 0 
Gene Names: IQGAP1KIAA0051
UniProt & NIH Common Fund Data Resources
Find proteins for P46940 (Homo sapiens)
Explore P46940 
Go to UniProtKB:  P46940
GTEx:  ENSG00000140575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46940
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.234 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.432α = 99.55
b = 66.421β = 104.07
c = 83.014γ = 108.69
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2016-11-16
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2023-07-26
    Changes: Database references
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description