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- EMDB-17603: Ligand-free SpSLC9C1 in detergent, asymmetric class -

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Basic information

Entry
Database: EMDB / ID: EMD-17603
TitleLigand-free SpSLC9C1 in detergent, asymmetric class
Map datadeepEMhancer sharpened map of ligand-free SpSLC9C1 in detergent, asymmetric class
Sample
  • Complex: Ligand-free SpSLC9C1 in detergent, asymmetric class
    • Protein or peptide: SpSLC9C1
KeywordsSLC9 / 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 / sperm flagellum / single fertilization / cAMP binding / potassium ion transmembrane transport / regulation of intracellular pH ...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 / regulation of intracellular pH / protein homodimerization activity / plasma membrane
Similarity search - Function
Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / 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 12, 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_17603.png

Downloads & links

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Map

FileDownload / File: emd_17603.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer sharpened map of ligand-free SpSLC9C1 in detergent, asymmetric class
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.0019402006 - 1.7387291
Average (Standard dev.)0.002228416 (±0.03479152)
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_17603_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: refined map of ligand-free SpSLC9C1 in detergent, asymmetric class

Fileemd_17603_additional_1.map
Annotationrefined map of ligand-free SpSLC9C1 in detergent, asymmetric class
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17603_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17603_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ligand-free SpSLC9C1 in detergent, asymmetric class

EntireName: Ligand-free SpSLC9C1 in detergent, asymmetric class
Components
  • Complex: Ligand-free SpSLC9C1 in detergent, asymmetric class
    • Protein or peptide: SpSLC9C1

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Supramolecule #1: Ligand-free SpSLC9C1 in detergent, asymmetric class

SupramoleculeName: Ligand-free SpSLC9C1 in detergent, asymmetric class / 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: SpSLC9C1

MacromoleculeName: SpSLC9C1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
SequenceString: 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

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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 mMNaCl
0.002 %GDN
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.
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
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3982593
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / 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: 598677
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0.)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.0.)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.1.0.)
FSC plot (resolution estimation)

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