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Yorodumi- PDB-8otq: Cryo-EM structure of Strongylocentrotus purpuratus sperm-specific... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8otq | ||||||
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Title | Cryo-EM structure of Strongylocentrotus purpuratus sperm-specific Na+/H+ exchanger SLC9C1 in GDN | ||||||
Components | Sperm-specific sodium proton exchanger | ||||||
Keywords | TRANSPORT PROTEIN / VSD / CNBD / Transporter / Voltage sensor / exchanger / sperm motility | ||||||
Function / homology | Function and homology information potassium:proton antiporter activity / sperm head / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / single fertilization / sperm flagellum / cAMP binding / cAMP-mediated signaling / potassium ion transmembrane transport ...potassium:proton antiporter activity / sperm head / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / single fertilization / sperm flagellum / cAMP binding / cAMP-mediated signaling / potassium ion transmembrane transport / regulation of intracellular pH / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Strongylocentrotus purpuratus (purple sea urchin) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å | ||||||
Authors | Yeo, H. / Mehta, V. / Gulati, A. / Drew, D. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nature / Year: 2023 Title: Structure and electromechanical coupling of a voltage-gated Na/H exchanger. Authors: Hyunku Yeo / Ved Mehta / Ashutosh Gulati / David Drew / Abstract: Voltage-sensing domains control the activation of voltage-gated ion channels, with a few exceptions. One such exception is the sperm-specific Na/H exchanger SLC9C1, which is the only known ...Voltage-sensing domains control the activation of voltage-gated ion channels, with a few exceptions. One such exception is the sperm-specific Na/H exchanger SLC9C1, which is the only known transporter to be regulated by voltage-sensing domains. After hyperpolarization of sperm flagella, SLC9C1 becomes active, causing pH alkalinization and CatSper Ca channel activation, which drives chemotaxis. SLC9C1 activation is further regulated by cAMP, which is produced by soluble adenyl cyclase (sAC). SLC9C1 is therefore an essential component of the pH-sAC-cAMP signalling pathway in metazoa, required for sperm motility and fertilization. Despite its importance, the molecular basis of SLC9C1 voltage activation is unclear. Here we report cryo-electron microscopy (cryo-EM) structures of sea urchin SLC9C1 in detergent and nanodiscs. We show that the voltage-sensing domains are positioned in an unusual configuration, sandwiching each side of the SLC9C1 homodimer. The S4 segment is very long, 90 Å in length, and connects the voltage-sensing domains to the cytoplasmic cyclic-nucleotide-binding domains. The S4 segment is in the up configuration-the inactive state of SLC9C1. Consistently, although a negatively charged cavity is accessible for Na to bind to the ion-transporting domains of SLC9C1, an intracellular helix connected to S4 restricts their movement. On the basis of the differences in the cryo-EM structure of SLC9C1 in the presence of cAMP, we propose that, upon hyperpolarization, the S4 segment moves down, removing this constriction and enabling Na/H exchange. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8otq.cif.gz | 461.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8otq.ent.gz | 339.6 KB | Display | PDB format |
PDBx/mmJSON format | 8otq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8otq_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8otq_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8otq_validation.xml.gz | 75.2 KB | Display | |
Data in CIF | 8otq_validation.cif.gz | 109.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/8otq ftp://data.pdbj.org/pub/pdb/validation_reports/ot/8otq | HTTPS FTP |
-Related structure data
Related structure data | 17182MC 8otwC 8otxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 147531.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Strongylocentrotus purpuratus (purple sea urchin) Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A3RL54 #2: Chemical | #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Homo-dimer of SLC9C1 transporter / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.294733 MDa / Experimental value: NO |
Source (natural) | Organism: Strongylocentrotus purpuratus (purple sea urchin) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293F |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 58.45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168016 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE | ||||||||||||||||||||||||
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