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Open data
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Basic information
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Title | cGMP-bound SpSLC9C1 in lipid nanodiscs, dimer | |||||||||||||||
![]() | deepEMhancer sharpened map of cGMP-bound SpSLC9C1 in lipid nanodiscs, used for model building and figure preparation | |||||||||||||||
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![]() | SLC9 / NHE / sperm-specific / ![]() | |||||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Kalienkova V / Peter M / Rheinberger J / Paulino C | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 91.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.8 KB 21.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 168.9 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() ![]() | 78.5 MB 79.3 MB 79.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pduMC ![]() 8pczC ![]() 8pd2C ![]() 8pd3C ![]() 8pd5C ![]() 8pd7C ![]() 8pd8C ![]() 8pd9C ![]() 8pdvC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | deepEMhancer sharpened map of cGMP-bound SpSLC9C1 in lipid nanodiscs, used for model building and figure preparation | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.022 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: refined map of cGMP-bound SpSLC9C1 in lipid nanodiscs,...
File | emd_17621_additional_1.map | ||||||||||||
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Annotation | refined map of cGMP-bound SpSLC9C1 in lipid nanodiscs, used for model refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17621_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17621_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : SpSLC9C1
Entire | Name: SpSLC9C1 |
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Components |
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-Supramolecule #1: SpSLC9C1
Supramolecule | Name: SpSLC9C1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Sperm-specific sodium proton exchanger
Macromolecule | Name: Sperm-specific sodium proton exchanger / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 147.624484 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: CYCLIC GUANOSINE MONOPHOSPHATE
Macromolecule | Name: CYCLIC GUANOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PCG |
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Molecular weight | Theoretical: 345.205 Da |
Chemical component information | ![]() ChemComp-PCG: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1.07 mg/mL | ||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: 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 | ||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 49407 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-60 / Number grids imaged: 4 / Number real images: 8482 / Average exposure time: 9.0 sec. / Average electron dose: 52.0 e/Å2 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |