9l5m | pdb_00009l5m

X-ray structure of sarcoplasmic Ca-binding protein (SCP), a calcium ion-binding protein from Pinctada fucata

spinqualitylabelsall models 9l5m, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9l5m is a 3 chain structure with sequence from Pinctada fucata. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2Å Ligands: CA Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Pf-SCP is an EF-hand protein identified in Pinctada fucata that is responsible for calcium transport and concentration in the mantle for shell formation. Previous studies have reported the calcium-binding properties of the EF-hand domains and the localization of Pf-SCP. To understand the calcification from Pf-SCP as a source of calcium, the dissociation of calcium from Pf-SCP must be investigated. However, calcium dissociation from EF-hand proteins, particularly in the presence of carbonate ions, remains poorly understood. In this study, we demonstrated that calcium dissociation from Pf-SCP was induced by carbonate ions using the fluorescence spectra of Pf-SCP, and this was followed by the synthesis of calcium carbonate that was characterized using scanning electron microscope-energy dispersive X-ray spectrometry (SEM-EDS). To gain insight into the calcium dissociation of Pf-SCP at the atomic level, we conducted molecular dynamics simulations using a multi-state ion model for calcium ions. The proposed mechanism of calcium dissociation in Pf-SCP is as follows: Water molecules first replace the amino acids in the EF-hand domain to coordinate calcium ions. Next, the carbonate ions bind to the calcium ions, decreasing the binding affinity of the EF-hand domains for the calcium ions. Finally, the calcium ions detach from the EF-hand, forming a complex with water molecules and carbonate ions. These findings provide a detailed understanding of the structural dynamics of calcium dissociation and the biomineralization mechanism in P. fucata, particularly in relation to the mantle calcification process. Calcium dissociation with carbonate ions from Pf-SCP, sarcoplasmic calcium-binding protein in Pinctada fucata, contributes to calcium mineralization for shell formation.,Namikawa Y, Zhu L, Lu P, Nagata K, Suzuki M Protein Sci. 2025 Nov;34(11):e70336. doi: 10.1002/pro.70336. PMID:41123418 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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