6N7E | pdb_00006n7e

Crystal structure of the cytosolic domain of human CNNM2 in complex with AMP-PNP and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.282 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.282 (Depositor), 0.241 (DCC) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Mg2+-ATP Sensing in CNNM, a Putative Magnesium Transporter.

Chen, Y.S.Kozlov, G.Fakih, R.Yang, M.Zhang, Z.Kovrigin, E.L.Gehring, K.

(2020) Structure 28: 324-335.e4

  • DOI: https://doi.org/10.1016/j.str.2019.11.016
  • Primary Citation Related Structures: 
    6MN6, 6N7E

  • PubMed Abstract: 

    The family of cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) is composed of four integral membrane proteins associated with Mg 2+ transport. Structurally, CNNMs contain large cytosolic regions composed of a CBS-pair and a cyclic nucleotide-binding homology (CNBH) domain. How these regulate Mg 2+ transport activity is unknown. Here, we determined the crystal structures of cytosolic fragments in two conformations: Mg 2+ -ATP-analog bound and ligand free. The structures reveal open and closed conformations with functionally important contacts not observed in structures of the individual domains. We also identified a second Mg 2+ -binding region in the CBS-pair domain and a different dimerization interface for the CNBH domain. Analytical ultracentrifugation and isothermal titration calorimetry experiments revealed a tight correlation between Mg 2+ -ATP binding and protein dimerization. Mutations that blocked either function prevented cellular Mg 2+ efflux activity. The results suggest Mg 2+ efflux is regulated by conformational changes associated with Mg 2+ -ATP binding to CNNM CBS-pair domains.


  • Organizational Affiliation
    • Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, QC H3G 0B1, Canada.

Macromolecule Content 

  • Total Structure Weight: 165.43 kDa 
  • Atom Count: 9,415 
  • Modeled Residue Count: 1,226 
  • Deposited Residue Count: 1,416 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metal transporter CNNM2,Metal transporter CNNM2
A, B, C, D
354Homo 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

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
L [auth C],
N [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
I [auth B]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
O [auth D],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.282 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.282 (Depositor), 0.241 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 290.582α = 90
b = 111.139β = 101.01
c = 103.519γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description