9DMR | pdb_00009dmr

Solution NMR structure of the calcium insensitive human LETM1 F-EF-hand domain mutant in the absence of calcium

• PDB DOI: https://doi.org/10.2210/pdb9DMR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-14 Released: 2025-05-07 
• Deposition Author(s): Lin, Q.T., Stathopulos, P.B.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

The apo LETM1 F-EF-hand adopts a closed conformation that underlies a multi-modal sensory role in mitochondria.

Lin, Q.T., Colussi, D.M., Stathopulos, P.B.

(2025) FEBS Lett 599: 971-988

• PubMed: 39927520 
• DOI: https://doi.org/10.1002/1873-3468.70006
• Primary Citation of Related Structures:  
  9DMR


• PubMed Abstract: 
  

  Leucine zipper EF-hand containing transmembrane protein-1 (LETM1) plays a critical role in mitochondrial function, with haploinsufficiency linked to Wolf-Hirschhorn syndrome. Here, we present the solution NMR structure of the calcium (Ca ²⁺ )-depleted LETM1 EF-hand domain, revealing a closed conformation facilitated by a distinct F ₁ -helix pivot rather than decreased interhelical angle. Further, we observe regiospecific unfolding in response to hot and cold denaturation and show H662 has a pKa in-line with physiological pH fluctuations. Finally, we demonstrate Ca ²⁺ -dependent transient interactions between the EF-hand and other LETM1 or GHITM protein domains. Collectively, our data reveal the apo-to-holo structural dynamics and mechanisms underlying the multi-modal sensing by the LETM1 EF-hand domain, highlighting its role as an adaptable regulatory element within the mitochondrial matrix.

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Organizational Affiliation: 
• Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 6.69 kDa 
• Atom Count: 466 
• Modeled Residue Count: 63 
• Deposited Residue Count: 63 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial proton/calcium exchanger protein	A	63	Homo sapiens	Mutation(s): 0  Gene Names: LETM1
UniProt & NIH Common Fund Data Resources
Find proteins for O95202 (Homo sapiens) Explore O95202  Go to UniProtKB:  O95202
PHAROS:  O95202 GTEx:  ENSG00000168924

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Lin, Q.T., Stathopulos, P.B.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	07171

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release