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- EMDB-41991: SLC9C1 at pH 6 in presence of Na+ -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41991
TitleSLC9C1 at pH 6 in presence of Na+
Map dataSharpened map from Relion Postprocess
Sample
  • Organelle or cellular component: WT sea urchin SLC9C1 at pH 6 in presence of Na+
    • Protein or peptide: Sperm-specific sodium proton exchanger
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: Digitonin
KeywordsMembrane transporter / SLC9 / voltage-sensitive / cAMP regulated / sperm capacitation / 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: 4.18 Å
AuthorsChowdhury S / Pal K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM145719 United States
CitationJournal: To Be Published
Title: SLC9C1 at pH 6 in presence of Na+
Authors: Chowdhury S / Pal K
History
DepositionSep 15, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41991.png

Downloads & links

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Map

FileDownload / File: emd_41991.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from Relion Postprocess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 180 pix.
= 248.4 Å		1.38 Å/pix.
x 180 pix.
= 248.4 Å		1.38 Å/pix.
x 180 pix.
= 248.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.021
Minimum - Maximum-0.09769905 - 0.17969283
Average (Standard dev.)0.0008975777 (±0.0052158404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 248.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41991_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map from Relion 3D Autorefine

Fileemd_41991_additional_1.map
AnnotationUnsharpened map from Relion 3D Autorefine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from Relion 3D Autorefine

Fileemd_41991_half_map_1.map
AnnotationHalf map 1 from Relion 3D Autorefine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from Relion 3D Autorefine

Fileemd_41991_half_map_2.map
AnnotationHalf map 2 from Relion 3D Autorefine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : WT sea urchin SLC9C1 at pH 6 in presence of Na+

EntireName: WT sea urchin SLC9C1 at pH 6 in presence of Na+
Components
  • Organelle or cellular component: WT sea urchin SLC9C1 at pH 6 in presence of Na+
    • Protein or peptide: Sperm-specific sodium proton exchanger
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: Digitonin

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Supramolecule #1: WT sea urchin SLC9C1 at pH 6 in presence of Na+

SupramoleculeName: WT sea urchin SLC9C1 at pH 6 in presence of Na+ / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Molecular weightTheoretical: 146.736484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 V

UniProtKB: Sperm-specific sodium:proton exchanger

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 3 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 3 / Number of copies: 4 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

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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

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1088719
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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