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- EMDB-17182: Cryo-EM structure of Strongylocentrotus purpuratus sperm-specific... -
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Open data
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Basic information
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Title | Cryo-EM structure of Strongylocentrotus purpuratus sperm-specific Na+/H+ exchanger SLC9C1 in GDN | |||||||||
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![]() | VSD / CNBD / Transporter / Voltage sensor / exchanger / sperm motility / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() sperm head / potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / cGMP binding / sperm flagellum / single fertilization / 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 / sperm flagellum / single fertilization / cAMP binding / potassium ion transmembrane transport / cAMP-mediated signaling / regulation of intracellular pH / protein homodimerization activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
![]() | Yeo H / Mehta V / Gulati A / Drew D | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 74.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.2 KB | Display | ![]() |
Images | ![]() | 144.4 KB | ||
Masks | ![]() | 149.9 MB | ![]() | |
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 132.3 MB 138.8 MB 138.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8otqMC ![]() 8otwC ![]() 8otxC 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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Voxel size | X=Y=Z: 1.0007 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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-Additional map: VSD CNBD monomer focused refinement map
File | emd_17182_additional_1.map | ||||||||||||
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Annotation | VSD_CNBD_monomer_focused_refinement_map | ||||||||||||
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-Half map: #2
File | emd_17182_half_map_1.map | ||||||||||||
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-Half map: #1
File | emd_17182_half_map_2.map | ||||||||||||
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Sample components
-Entire : Homo-dimer of SLC9C1 transporter
Entire | Name: Homo-dimer of SLC9C1 transporter |
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Components |
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-Supramolecule #1: Homo-dimer of SLC9C1 transporter
Supramolecule | Name: Homo-dimer of SLC9C1 transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 294.733 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: 147.531328 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKKRVVKLRE LVPAVAALAV AVLIQSATGS SGGSGHTPTT QATHADDHDL TTHNGTEEHD DGHDDGHDDL HAHAPKVIVF ISGSCLFGA ISRSLFKKLP IPYTVVLLIL GAILGVVASN VPLVEEHTRD VAHMDPHVLL QIFLPVLIFE SAFAMDVHTF M RSFSQVCI ...String: MKKRVVKLRE LVPAVAALAV AVLIQSATGS SGGSGHTPTT QATHADDHDL TTHNGTEEHD DGHDDGHDDL HAHAPKVIVF ISGSCLFGA ISRSLFKKLP IPYTVVLLIL GAILGVVASN VPLVEEHTRD VAHMDPHVLL QIFLPVLIFE SAFAMDVHTF M RSFSQVCI LALFGLVVAS VLTAVLAMNL FNYNWNFSEA MMFGAIMSAT DPVAVVALLK DLGASKQLGT IIEGESLLND GC AIVIFNV FMKMVFFPQL TSTVGQNVLY FLQVAVAGPL WGYAVAKVTV FFLSHIFNDA LVEITITLAA TYLTYYIGDI WLE VSGVLA VVVLGLIVNA EKTSISPEVE VFLHRFWEML AYLANTLIFM MVGVVVTQKA LVAVDKMDWF YLIILYLAIT IIRG MVISL FSPILSRIGY GLTWRNAVIM TWGGLRGAVG LALALVVENL AGNDVIGSKF LFHTAGIVVL TLVINATTIQ TLLRI LGMS DISIPKRLAM AGAVRRIHEG QNRTLNMLKS DRFLADADWD IATAACEISD PYSALSDDEN APADELTLGE RKSVCP GCK AMVPNEPSPR EFADMMEEAR LRMLKAEKIS YWKQFEHGML AREALRLLVQ HAEVAADEKD QFILVDDLKK SWQIKGI YP WLKRKLEDLI SEKKIAAIPM PKYKLGKLMY KICHHMAFEV TINIAIVLNI VPIIMEFVVQ DKMASVSTMA APGSTVSS E PSSLQKIEDA LRISNYVFFV IYAIEAIVKI LGLGRHYIVS HWNKFDAFIL VVALVDIIIA ETLLKGSITI NLSSIKVVK LFRLLRGLRM LRLTKALIPK LILVVNGKIN NQLSLGYDVG KGYIIGEEEV GKIIDRMVDN KKILRELKHI SETGRLQVVK ELGLLQREH PGIAVSVKTR QAIRTILNHS RETIHELQGA GLLDEMEAHK LELTVEIKMK RLMNAPSSIP PPPPENLLKN V SWLAGDMK LIDFIKARAS LLHFDYGEVI VREGDESDGL FLIVSGLVKL YGKSAFLDHD NPPVTAGSEE NEVFEDYLTV GN VIGEMGV LTKKPRNATV TCETTVQVYF ITAEDMNIAI DTFTLYPSLE YRLWRVVAIR IATPLIMEQM AFQGWTQEKV KLH LERGYL VDLAESHFQF NIDATLEDVI LINGTAYNAH TREEIRSPCL ISRTVHKLTF QYTATEEPRL FVVRNAEYNG PILD GRLDV DSKRSLISIT EISSNMCLKH AAELRQKNSK VMLSRKSSGA AAKEEEDCIP NTSDVEQAAG VSPSVPTKTT PKPKS FLPS LGLSMSKERV NGEAVEESPV KTKQGEETPE TEEGAAPRVN VENLYFQ UniProtKB: Sperm-specific sodium:proton exchanger |
-Macromolecule #2: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: CPL |
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Molecular weight | Theoretical: 758.06 Da |
Chemical component information | ![]() ChemComp-CPL: |
-Macromolecule #3: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.45 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |