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- EMDB-17599: Ligand-free SpSLC9C1 in lipid nanodiscs, protomer state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-17599
TitleLigand-free SpSLC9C1 in lipid nanodiscs, protomer state 2
Map data
Sample
  • Complex: Ligand-free SpSLC9C1 in lipid nanodiscs, monomeric state 2
    • Protein or peptide: Sperm-specific sodium proton exchanger
KeywordsSLC9 / NHE / sperm-specific / MEMBRANE PROTEIN
Function / homology
Function and homology information


potassium:proton antiporter activity / sperm head / sodium:proton antiporter activity / sodium ion import across plasma membrane / cAMP-mediated signaling / cGMP binding / sperm flagellum / cAMP binding / potassium ion transmembrane transport / regulation of intracellular pH ...potassium:proton antiporter activity / sperm head / sodium:proton antiporter activity / sodium ion import across plasma membrane / cAMP-mediated signaling / cGMP binding / sperm flagellum / cAMP binding / potassium ion transmembrane transport / regulation of intracellular pH / protein homodimerization activity / plasma membrane
Similarity search - Function
Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Voltage-dependent channel domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Sperm-specific sodium:proton exchanger
Similarity search - Component
Biological speciesStrongylocentrotus purpuratus (purple sea urchin)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKalienkova V / Peter M / Rheinberger J / Paulino C
Funding support Netherlands, Switzerland, 4 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)722.017.001 Netherlands
Netherlands Organisation for Scientific Research (NWO)740.018.016 Netherlands
Swiss National Science FoundationP500PB_203053 Switzerland
Swiss National Science FoundationP2ZHP3_187679 Switzerland
CitationJournal: Nature / Year: 2023
Title: Structures of a sperm-specific solute carrier gated by voltage and cAMP.
Authors: Valeria Kalienkova / Martin F Peter / Jan Rheinberger / Cristina Paulino /
Abstract: The newly characterized sperm-specific Na/H exchanger stands out by its unique tripartite domain composition. It unites a classical solute carrier unit with regulatory domains usually found in ion ...The newly characterized sperm-specific Na/H exchanger stands out by its unique tripartite domain composition. 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, 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, our structure represents a potential new platform for the development of new on-demand contraceptives.
History
DepositionJun 11, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17599.png

Downloads & links

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Map

FileDownload / File: emd_17599.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 250.8 Å		0.84 Å/pix.
x 300 pix.
= 250.8 Å		0.84 Å/pix.
x 300 pix.
= 250.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

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Histogram (log scale)
Contour LevelBy AUTHOR: 0.056
Minimum - Maximum-0.0018104777 - 1.5947078
Average (Standard dev.)0.0014502391 (±0.026781414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 250.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17599_msk_1.map
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Additional map: #1

Fileemd_17599_additional_1.map
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Half map: #2

Fileemd_17599_half_map_1.map
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Half map: #1

Fileemd_17599_half_map_2.map
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Sample components

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Entire : Ligand-free SpSLC9C1 in lipid nanodiscs, monomeric state 2

EntireName: Ligand-free SpSLC9C1 in lipid nanodiscs, monomeric state 2
Components
  • Complex: Ligand-free SpSLC9C1 in lipid nanodiscs, monomeric state 2
    • Protein or peptide: Sperm-specific sodium proton exchanger

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Supramolecule #1: Ligand-free SpSLC9C1 in lipid nanodiscs, monomeric state 2

SupramoleculeName: Ligand-free SpSLC9C1 in lipid nanodiscs, monomeric state 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Sperm-specific sodium proton exchanger

MacromoleculeName: Sperm-specific sodium proton exchanger / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Molecular weightTheoretical: 147.624484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKKRVVKLR ELVPAVAALA VAVLIQSATG SSGGSGHTPT TQATHADDHD LTTHNGTEEH DDGHDDGHDD LHAHAPKVIV FISGSCLFG AISRSLFKKL PIPYTVVLLI LGAILGVVAS NVPLVEEHTR DVAHMDPHVL LQIFLPVLIF ESAFAMDVHT F MRSFSQVC ...String:
MSKKRVVKLR ELVPAVAALA VAVLIQSATG SSGGSGHTPT TQATHADDHD LTTHNGTEEH DDGHDDGHDD LHAHAPKVIV FISGSCLFG AISRSLFKKL PIPYTVVLLI LGAILGVVAS NVPLVEEHTR DVAHMDPHVL LQIFLPVLIF ESAFAMDVHT F MRSFSQVC ILALFGLVVA SVLTAVLAMN LFNYNWNFSE AMMFGAIMSA TDPVAVVALL KDLGASKQLG TIIEGESLLN DG CAIVIFN VFMKMVFFPQ LTSTVGQNVL YFLQVAVAGP LWGYAVAKVT VFFLSHIFND ALVEITITLA ATYLTYYIGD IWL EVSGVL AVVVLGLIVN AEKTSISPEV EVFLHRFWEM LAYLANTLIF MMVGVVVTQK ALVAVDKMDW FYLIILYLAI TIIR GMVIS LFSPILSRIG YGLTWRNAVI MTWGGLRGAV GLALALVVEN LAGNDVIGSK FLFHTAGIVV LTLVINATTI QTLLR ILGM SDISIPKRLA MAGAVRRIHE GQNRTLNMLK SDRFLADADW DIATAACEIS DPYSALSDDE NAPADELTLG ERKSVC PGC KAMVPNEPSP REFADMMEEA RLRMLKAEKI SYWKQFEHGM LAREALRLLV QHAEVAADEK DQFILVDDLK KSWQIKG IY PWLKRKLEDL ISEKKIAAIP MPKYKLGKLM YKICHHMAFE VTINIAIVLN IVPIIMEFVV QDKMASVSTM AAPGSTVS S EPSSLQKIED ALRISNYVFF VIYAIEAIVK ILGLGRHYIV SHWNKFDAFI LVVALVDIII AETLLKGSIT INLSSIKVV KLFRLLRGLR MLRLTKALIP KLILVVNGKI NNQLSLGYDV GKGYIIGEEE VGKIIDRMVD NKKILRELKH ISETGRLQVV KELGLLQRE HPGIAVSVKT RQAIRTILNH SRETIHELQG AGLLDEMEAH KLELTVEIKM KRLMNAPSSI PPPPPENLLK N VSWLAGDM KLIDFIKARA SLLHFDYGEV IVREGDESDG LFLIVSGLVK LYGKSAFLDH DNPPVTAGSE ENEVFEDYLT VG NVIGEMG VLTKKPRNAT VTCETTVQVY FITAEDMNIA IDTFTLYPSL EYRLWRVVAI RIATPLIMEQ MAFQGWTQEK VKL HLERGY LVDLAESHFQ FNIDATLEDV ILINGTAYNA HTREEIRSPC LISRTVHKLT FQYTATEEPR LFVVRNAEYN GPIL DGRLD VDSKRSLISI TEISSNMCLK HAAELRQKNS KVMLSRKSSG AAAKEEEDCI PNTSDVEQAA GVSPSVPTKT TPKPK SFLP SLGLSMSKER VNGEAVEESP VKTKQGEETP ETEEGAAPRV NVALEVLFQ

UniProtKB: Sperm-specific sodium:proton exchanger

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.93 mg/mL
BufferpH: 7.6
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: at 5 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 59809 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11299 / Average exposure time: 2.51 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5022107
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0.)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.1.0.)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0.)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0.) / Number images used: 379058
FSC plot (resolution estimation)

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