6PW7

X-ray crystal structure of C. elegans STIM EF-SAM domain

Summary for 6PW7

• Entry DOI: 10.2210/pdb6pw7/pdb
• Descriptor: Stromal interaction molecule 1, CALCIUM ION (3 entities in total)
• Functional Keywords: stromal interaction molecule (stim), ef-hand, sam-domain, calcium release-activated channels, store operated calcium entry (soce), signaling protein
• Biological source: Caenorhabditis elegans
• Total number of polymer chains: 2
• Total formula weight: 38155.45

Authors

Enomoto, M.,Nishikawa, T.,Back, S.I.,Ishiyama, N.,Zheng, L.,Stathopulos, P.B.,Ikura, M. (deposition date: 2019-07-22, release date: 2019-11-13, Last modification date: 2020-02-12)

Primary citation

Enomoto, M.,Nishikawa, T.,Back, S.I.,Ishiyama, N.,Zheng, L.,Stathopulos, P.B.,Ikura, M.
Coordination of a Single Calcium Ion in the EF-hand Maintains the Off State of the Stromal Interaction Molecule Luminal Domain.
J.Mol.Biol., 432:367-383, 2020

PubMed Abstract: Store operated calcium (Ca) entry (SOCE) is the process whereby endoplasmic reticulum (ER) Ca store depletion causes Orai1-composed Ca channels on the plasma membrane (PM) to open, mediating a rise in cytosolic Ca levels. Stromal interaction molecules (STIMs) are the proteins that directly sense ER Ca content and gate Orai1 channels due to store depletion. The trigger for STIM activation is Ca unbinding from the ER lumen-oriented domains, which consist of a nonconserved amino (N) terminal region and EF-hand and sterile α motif (SAM) domains (EF-SAM), highly conserved from humans to Caenorhabditis elegans. Solution NMR structures of the human EF-SAM domains have been determined at high Ca concentrations; however, no direct structural view of the Ca binding mode has been elucidated. Further, no atomic resolution data currently exists on EF-SAM at low Ca levels. Here, we determined the X-ray crystal structure of the C. elegans STIM luminal domain, revealing that EF-SAM binds a single Ca ion with pentagonal bipyramidal geometry and an ancillary α-helix formed by the N-terminal region acts as a brace to stabilize EF-SAM. Using solution NMR, we observed EF-hand domain unfolding and a conformational exchange between folded and unfolded states involving the ancillary α-helix and the canonical EF-hand in low Ca. Remarkably, we also detected an α-helix (+Ca) to β-strand (-Ca) transition at the terminal SAM domain α-helix. Collectively, our analyses indicate that one canonically bound Ca ion is sufficient to stabilize the quiescent luminal domain structure, precluding unfolding, conformational exchange, and secondary structure transformation.

PubMed: 31626806
DOI: 10.1016/j.jmb.2019.10.003

Experimental method

X-RAY DIFFRACTION (1.89 Å)