9BA1 image
Entry Detail
PDB ID:
9BA1
Title:
Solution NMR structure of the human LETM1 F-EF-hand domain in the presence of calcium
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-04-03
Release Date:
2024-10-16
Method Details:
Experimental Method:
Conformers Calculated:
200
Conformers Submitted:
10
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Mitochondrial proton/calcium exchanger protein
Chain IDs:A
Chain Length:63
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
An AI-informed NMR structure reveals an extraordinary LETM1 F-EF-hand domain that functions as a two-way regulator of mitochondrial calcium.
Structure 32 2063 ? (2024)
PMID: 39317198 DOI: 10.1016/j.str.2024.08.020

Abstact

AlphaFold can accurately predict static protein structures but does not account for solvent conditions. Human leucine zipper EF-hand transmembrane protein-1 (LETM1) has one sequence-identifiable EF-hand but how calcium (Ca2+) affects structure and function remains enigmatic. Here, we used highly confident AlphaFold Cα predictions to guide nuclear Overhauser effect (NOE) assignments and structure calculation of the LETM1 EF-hand in the presence of Ca2+. The resultant NMR structure exposes pairing between a partial loop-helix and full helix-loop-helix, forming an unprecedented F-EF-hand with non-canonical Ca2+ coordination but enhanced hydrophobicity for protein interactions compared to calmodulin. The structure also reveals the basis for pH sensing at the link between canonical and partial EF-hands. Functionally, mutations that augmented or weakened Ca2+ binding increased or decreased matrix Ca2+, respectively, establishing F-EF as a two-way mitochondrial Ca2+ regulator. Thus, we show how to synergize AI prediction with NMR data, elucidating a solution-specific and extraordinary LETM1 F-EF-hand.

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