8RX8 | pdb_00008rx8

The structure of CML18 in complex with 4 Ca2+ ions

• PDB DOI: https://doi.org/10.2210/pdb8RX8/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-06 Released: 2024-10-09 
• Deposition Author(s): Daniel-Mozo, M., Albert, A.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.285 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Models: experimental

Literature

The vacuolar K + /H + exchangers and calmodulin-like CML18 constitute a pH-sensing module that regulates K + status in Arabidopsis.

Daniel-Mozo, M., Rombola-Caldentey, B., Mendoza, I., Ragel, P., De Luca, A., Carranco, R., Alcaide, A.M., Ausili, A., Cubero, B., Schumacher, K., Quintero, F.J., Albert, A., Pardo, J.M.

(2024) Sci Adv 10: eadp7658-eadp7658

• PubMed: 39536104 
• DOI: https://doi.org/10.1126/sciadv.adp7658
• Primary Citation of Related Structures:  
  8RX8


• PubMed Abstract: 
  

  Shifts in cytosolic pH have been recognized as key signaling events and mounting evidence supports the interdependence between H ⁺ and Ca ²⁺ signaling in eukaryotic cells. Among the cellular pH-stats, K ⁺ /H ⁺ exchange at various membranes is paramount in plant cells. Vacuolar K ⁺ /H ⁺ exchangers of the NHX (Na ⁺ ,K ⁺ /H ⁺ exchanger) family control luminal pH and, together with K ⁺ and H ⁺ transporters at the plasma membrane, have been suggested to also regulate cytoplasmic pH. We show the regulation of vacuolar K ⁺ /H ⁺ exchange by cytoplasmic pH and the calmodulin-like protein CML18 in Arabidopsis. The crystal structure and physicochemical properties of CML18 indicate that this protein senses pH shifts. Interaction of CML18 with tonoplast exchangers NHX1 and NHX2 was favored at acidic pH, a physiological condition elicited by K ⁺ starvation in Arabidopsis roots, whereas excess K ⁺ produced cytoplasmic alkalinization and CML18 dissociation. These results imply that the pH-responsive NHX-CML18 module is an essential component of the cellular K ⁺ - and pH-stats.

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Organizational Affiliation: 
• Instituto de Química Física Blas Cabrera, Consejo Superior de Investigaciones Científicas, Madrid 28006, Spain.
Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas and University of Seville, Seville 41092, Spain.
Centre for Organismal Studies, University of Heidelberg, Heidelberg 69120, Germany.
Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Cientificas, Seville 41012, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.27 kDa 
• Atom Count: 1,188 
• Modeled Residue Count: 152 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable calcium-binding protein CML18	A	165	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CML18, CAM15, At3g03000, F13E7.5
UniProt
Find proteins for Q9M8U1 (Arabidopsis thaliana) Explore Q9M8U1  Go to UniProtKB:  Q9M8U1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.285 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.34	α = 90
b = 74.34	β = 90
c = 131.33	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
Coot	model building
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Daniel-Mozo, M., Albert, A.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2020-119805RB-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	PRE2018-083280

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Database references