+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17604 | |||||||||||||||
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Title | Ligand-free SpSLC9C1 in detergent, symmetric class | |||||||||||||||
Map data | deepEMhancer sharpened map of ligand-free SpSLC9C1 in detergent, symmetric class | |||||||||||||||
Sample |
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Keywords | SLC9 / NHE / sperm-specific / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information sperm head / potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / single fertilization / sperm flagellum / cAMP binding / potassium ion transmembrane transport / cAMP-mediated signaling ...sperm head / potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / single fertilization / sperm flagellum / cAMP binding / potassium ion transmembrane transport / cAMP-mediated signaling / regulation of intracellular pH / protein homodimerization activity / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Strongylocentrotus purpuratus (purple sea urchin) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||||||||
Authors | Kalienkova V / Peter M / Rheinberger J / Paulino C | |||||||||||||||
Funding support | Netherlands, Switzerland, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17604.map.gz | 91.5 MB | EMDB map data format | |
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Header (meta data) | emd-17604-v30.xml emd-17604.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17604_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_17604.png | 145.8 KB | ||
Masks | emd_17604_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-17604.cif.gz | 6.2 KB | ||
Others | emd_17604_additional_1.map.gz emd_17604_half_map_1.map.gz emd_17604_half_map_2.map.gz | 78 MB 79.2 MB 79.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17604 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17604 | HTTPS FTP |
-Validation report
Summary document | emd_17604_validation.pdf.gz | 750.6 KB | Display | EMDB validaton report |
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Full document | emd_17604_full_validation.pdf.gz | 750.2 KB | Display | |
Data in XML | emd_17604_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_17604_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17604 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17604 | HTTPS FTP |
-Related structure data
Related structure data | 8pczC 8pd2C 8pd3C 8pd5C 8pd7C 8pd8C 8pd9C 8pduC 8pdvC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17604.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | deepEMhancer sharpened map of ligand-free SpSLC9C1 in detergent, symmetric class | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.836 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17604_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: refined map of ligand-free SpSLC9C1 in detergent, symmetric class
File | emd_17604_additional_1.map | ||||||||||||
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Annotation | refined map of ligand-free SpSLC9C1 in detergent, symmetric class | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17604_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17604_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: all |
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Source (natural) | Organism: Strongylocentrotus purpuratus (purple sea urchin) |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: SpSLC9C1
Macromolecule | Name: SpSLC9C1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Strongylocentrotus purpuratus (purple sea urchin) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSKKRVVKLR ELVPAVAALA VAVLIQSATG SSGGSGHTPT TQATHADDHD LTTHNGTEEH DDGHDDGHDD LHAHAPKVIV FISGSCLFGA ISRSLFKKLP IPYTVVLLIL GAILGVVASN VPLVEEHTRD VAHMDPHVLL QIFLPVLIFE SAFAMDVHTF MRSFSQVCIL ...String: MSKKRVVKLR ELVPAVAALA VAVLIQSATG SSGGSGHTPT TQATHADDHD LTTHNGTEEH DDGHDDGHDD LHAHAPKVIV FISGSCLFGA ISRSLFKKLP IPYTVVLLIL GAILGVVASN VPLVEEHTRD VAHMDPHVLL QIFLPVLIFE SAFAMDVHTF MRSFSQVCIL ALFGLVVASV LTAVLAMNLF NYNWNFSEAM MFGAIMSATD PVAVVALLKD LGASKQLGTI IEGESLLNDG CAIVIFNVFM KMVFFPQLTS TVGQNVLYFL QVAVAGPLWG YAVAKVTVFF LSHIFNDALV EITITLAATY LTYYIGDIWL EVSGVLAVVV LGLIVNAEKT SISPEVEVFL HRFWEMLAYL ANTLIFMMVG VVVTQKALVA VDKMDWFYLI ILYLAITIIR GMVISLFSPI LSRIGYGLTW RNAVIMTWGG LRGAVGLALA LVVENLAGND VIGSKFLFHT AGIVVLTLVI NATTIQTLLR ILGMSDISIP KRLAMAGAVR RIHEGQNRTL NMLKSDRFLA DADWDIATAA CEISDPYSAL SDDENAPADE LTLGERKSVC PGCKAMVPNE PSPREFADMM EEARLRMLKA EKISYWKQFE HGMLAREALR LLVQHAEVAA DEKDQFILVD DLKKSWQIKG IYPWLKRKLE DLISEKKIAA IPMPKYKLGK LMYKICHHMA FEVTINIAIV LNIVPIIMEF VVQDKMASVS TMAAPGSTVS SEPSSLQKIE DALRISNYVF FVIYAIEAIV KILGLGRHYI VSHWNKFDAF ILVVALVDII IAETLLKGSI TINLSSIKVV KLFRLLRGLR MLRLTKALIP KLILVVNGKI NNQLSLGYDV GKGYIIGEEE VGKIIDRMVD NKKILRELKH ISETGRLQVV KELGLLQREH PGIAVSVKTR QAIRTILNHS RETIHELQGA GLLDEMEAHK LELTVEIKMK RLMNAPSSIP PPPPENLLKN VSWLAGDMKL IDFIKARASL LHFDYGEVIV REGDESDGLF LIVSGLVKLY GKSAFLDHDN PPVTAGSEEN EVFEDYLTVG NVIGEMGVLT KKPRNATVTC ETTVQVYFIT AEDMNIAIDT FTLYPSLEYR LWRVVAIRIA TPLIMEQMAF QGWTQEKVKL HLERGYLVDL AESHFQFNID ATLEDVILIN GTAYNAHTRE EIRSPCLISR TVHKLTFQYT ATEEPRLFVV RNAEYNGPIL DGRLDVDSKR SLISITEISS NMCLKHAAEL RQKNSKVMLS RKSSGAAAKE EEDCIPNTSD VEQAAGVSPS VPTKTTPKPK SFLPSLGLSM SKERVNGEAV EESPVKTKQG EETPETEEGA APRVNVALEV LFQ UniProtKB: Sperm-specific sodium:proton exchanger |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 7090 / Average exposure time: 2.31 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 59809 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |