Crystal structure of CNNM3 cyclic nucleotide-binding homology domain

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

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The cyclic nucleotide-binding homology domain of the integral membrane protein CNNM mediates dimerization and is required for Mg2+efflux activity.

Chen, Y.S.Kozlov, G.Fakih, R.Funato, Y.Miki, H.Gehring, K.

(2018) J Biol Chem 293: 19998-20007

  • DOI: https://doi.org/10.1074/jbc.RA118.005672
  • Primary Citation of Related Structures:  
    6DFD, 6DJ3

  • PubMed Abstract: 

    Proteins of the cyclin M family (CNNMs; also called ancient conserved domain proteins, or ACDPs) are represented by four integral membrane proteins that have been proposed to function as Mg 2+ transporters. CNNMs are associated with a number of genetic diseases affecting ion movement and cancer via their association with highly oncogenic phosphatases of regenerating liver (PRLs). Structurally, CNNMs contain an N-terminal extracellular domain, a transmembrane domain (DUF21), and a large cytosolic region containing a cystathionine-β-synthase (CBS) domain and a putative cyclic nucleotide-binding homology (CNBH) domain. Although the CBS domain has been extensively characterized, little is known about the CNBH domain. Here, we determined the first crystal structures of the CNBH domains of CNNM2 and CNNM3 at 2.6 and 1.9 Å resolutions. Contrary to expectation, these domains did not bind cyclic nucleotides, but mediated dimerization both in crystals and in solution. Analytical ultracentrifugation experiments revealed an inverse correlation between the propensity of the CNBH domains to dimerize and the ability of CNNMs to mediate Mg 2+ efflux. CNBH domains from active family members were observed as both dimers and monomers, whereas the inactive member, CNNM3, was observed only as a dimer. Mutational analysis revealed that the CNBH domain was required for Mg 2+ efflux activity of CNNM4. This work provides a structural basis for understanding the function of CNNM proteins in Mg 2+ transport and associated diseases.

  • Organizational Affiliation

    From the Department of Biochemistry and Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metal transporter CNNM3
A, B
260Homo sapiensMutation(s): 6 
Gene Names: CNNM3ACDP3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NE01 (Homo sapiens)
Explore Q8NE01 
Go to UniProtKB:  Q8NE01
GTEx:  ENSG00000168763 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NE01
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.267α = 90
b = 101.267β = 90
c = 77.12γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references