8PD3

Ligand-free SpSLC9C1 in lipid nanodiscs, protomer state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of a sperm-specific solute carrier gated by voltage and cAMP.

Kalienkova, V.Peter, M.F.Rheinberger, J.Paulino, C.

(2023) Nature 623: 202-209

  • DOI: https://doi.org/10.1038/s41586-023-06629-w
  • Primary Citation of Related Structures:  
    8PCZ, 8PD2, 8PD3, 8PD5, 8PD7, 8PD8, 8PD9, 8PDU, 8PDV

  • PubMed Abstract: 

    The newly characterized sperm-specific Na + /H + exchanger stands out by its unique tripartite domain composition 1,2 . It unites a classical solute carrier unit with regulatory domains usually found in ion channels, namely, a voltage-sensing domain and a cyclic-nucleotide binding domain 1,3 , which makes it a mechanistic chimera and a secondary-active transporter activated strictly by membrane voltage. Our structures of the sea urchin SpSLC9C1 in the absence and presence of ligands reveal the overall domain arrangement and new structural coupling elements. They allow us to propose a gating model, where movements in the voltage sensor indirectly cause the release of the exchanging unit from a locked state through long-distance allosteric effects transmitted by the newly characterized coupling helices. We further propose that modulation by its ligand cyclic AMP occurs by means of disruption of the cytosolic dimer interface, which lowers the energy barrier for S4 movements in the voltage-sensing domain. As SLC9C1 members have been shown to be essential for male fertility, including in mammals 2,4,5 , our structure represents a potential new platform for the development of new on-demand contraceptives.


  • Organizational Affiliation

    Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm-specific sodium proton exchanger1,333Strongylocentrotus purpuratusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A3RL54 (Strongylocentrotus purpuratus)
Explore A3RL54 
Go to UniProtKB:  A3RL54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3RL54
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.0.

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands722.017.001
Netherlands Organisation for Scientific Research (NWO)Netherlands740.018.016
Swiss National Science FoundationSwitzerlandP500PB_203053
Swiss National Science FoundationSwitzerlandP2ZHP3_187679

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references