9EVC | pdb_00009evc

CryoEM structure of LMCA1 in E1-Ca state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dephosphorylation and ion binding in prokaryotic calcium transport.

Prabudiansyah, I.Oradd, F.Magkakis, K.Pounot, K.Levantino, M.Andersson, M.

(2024) Sci Adv 10: eadp2916-eadp2916

  • DOI: https://doi.org/10.1126/sciadv.adp2916
  • Primary Citation of Related Structures:  
    9EUQ, 9EVC

  • PubMed Abstract: 

    Calcium (Ca 2+ ) signaling is fundamental to cellular processes in both eukaryotic and prokaryotic organisms. While the mechanisms underlying eukaryotic Ca 2+ transport are well documented, an understanding of prokaryotic transport remains nascent. LMCA1, a Ca 2+ adenosine triphosphatase (ATPase) from Listeria monocytogenes , has emerged as a prototype for elucidating structure and dynamics in prokaryotic Ca 2+ transport. Here, we used a multidisciplinary approach integrating kinetics, structure, and dynamics to unravel the intricacies of LMCA1 function. A cryo-electron microscopy (cryo-EM) structure of a Ca 2+ -bound E1 state showed ion coordination by Asp 720 , Asn 716 , and Glu 292 . Time-resolved x-ray solution scattering experiments identified phosphorylation as the rate-determining step. A cryo-EM E2P state structure exhibited remarkable similarities to a SERCA1a E2-P* state, which highlights the essential role of the unique P-A domain interface in enhancing dephosphorylation rates and reconciles earlier proposed mechanisms. Our study underscores the distinctiveness between eukaryotic and prokaryotic Ca 2+ ATPase transport systems and positions LMCA1 as a promising drug target for developing antimicrobial strategies.


  • Organizational Affiliation
    • Department of Chemistry, Umeå University, Umeå, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium-transporting ATPase lmo0841880Listeria monocytogenesMutation(s): 0 
Gene Names: lmo0841
EC: 7.2.2.10
Membrane Entity: Yes 
UniProt
Find proteins for Q8Y8Q5 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y8Q5 
Go to UniProtKB:  Q8Y8Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y8Q5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection