8F6D | pdb_00008f6d

Crystal structure of the CNNM2 CBS-pair domain in complex with ARL15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.293 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.264 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8F6D

This is version 1.2 of the entry. See complete history

Literature

Structural insights into regulation of CNNM-TRPM7 divalent cation uptake by the small GTPase ARL15.

Mahbub, L.Kozlov, G.Zong, P.Lee, E.L.Tetteh, S.Nethramangalath, T.Knorn, C.Jiang, J.Shahsavan, A.Yue, L.Runnels, L.Gehring, K.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.86129
  • Primary Citation Related Structures: 
    8F6D

  • PubMed Abstract: 

    Cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg 2+ ions on their own and influx of divalent cations when expressed with the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM-binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP and CNNM-binding protein and demonstrate that ARL15 also inhibits CNNM2 Mg 2+ efflux. The crystal structure of a complex between ARL15 and CNNM2 CBS-pair domain reveals the molecular basis for binding and allowed the identification of mutations that specifically block binding. A binding deficient ARL15 mutant, R95A, failed to inhibit CNNM and TRPM7 transport of Mg 2+ and Zn 2+ ions. Structural analysis and binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) showed that ARL15 and PRLs compete for binding CNNM to coordinate regulation of ion transport by CNNM and TRPM7.


  • Organizational Affiliation
    • Department of Biochemistry, McGill University, Montreal, Canada.

Macromolecule Content 

  • Total Structure Weight: 149.28 kDa 
  • Atom Count: 7,791 
  • Modeled Residue Count: 1,146 
  • Deposited Residue Count: 1,316 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metal transporter CNNM2
A, C, E, G
156Homo sapiensMutation(s): 0 
Gene Names: CNNM2ACDP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8M5 (Homo sapiens)
Explore Q9H8M5 
Go to UniProtKB:  Q9H8M5
PHAROS:  Q9H8M5
GTEx:  ENSG00000148842 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H8M5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosylation factor-like protein 15
B, D, F, H
173Homo sapiensMutation(s): 0 
Gene Names: ARL15ARFRP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXU5 (Homo sapiens)
Explore Q9NXU5 
Go to UniProtKB:  Q9NXU5
PHAROS:  Q9NXU5
GTEx:  ENSG00000185305 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXU5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.293 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.264 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.018α = 94.353
b = 73.323β = 95.5
c = 79.327γ = 115.33
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-01-24
    Changes: Database references