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- EMDB-38565: Structure of the sea urchin spSLC9C1 in state-2 w/o cAMP protomer -

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Basic information

Entry
Database: EMDB / ID: EMD-38565
TitleStructure of the sea urchin spSLC9C1 in state-2 w/o cAMP protomer
Map datamap of spSLC9C1 state-2 protomer
Sample
  • Organelle or cellular component: solute carrier 9C1 protomer
    • Protein or peptide: Sperm-specific sodium proton exchanger
KeywordsSodium-hydrogen exchanger / TRANSPORT 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
Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / 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: 3.21 Å
AuthorsQu H / Zheng X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371292 China
CitationJournal: Cell Insight / Year: 2024
Title: Structures of a sperm-specific sodium-hydrogen exchanger.
Authors: Hongyuan Qu / Yi Zhen / Mohan Xu / Yan Huang / Yashu Wang / Gaoyuan Ji / Yuyu Zhang / Haitao Li / Zigang Dong / Xiangdong Zheng /
History
DepositionJan 4, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38565.png

Downloads & links

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Map

FileDownload / File: emd_38565.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of spSLC9C1 state-2 protomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.162
Minimum - Maximum-0.001683834 - 1.6710614
Average (Standard dev.)0.0010201975 (±0.023080489)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: map of spSLC9C1 state-2 protomer

Fileemd_38565_half_map_1.map
Annotationmap of spSLC9C1 state-2 protomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_38565_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : solute carrier 9C1 protomer

EntireName: solute carrier 9C1 protomer
Components
  • Organelle or cellular component: solute carrier 9C1 protomer
    • Protein or peptide: Sperm-specific sodium proton exchanger

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Supramolecule #1: solute carrier 9C1 protomer

SupramoleculeName: solute carrier 9C1 protomer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Molecular weightTheoretical: 144.950125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSSSGGSGHT PTTQATHADD HDLTTHNGTE EHDDGHDDGH DDLHAHAPKV IVFISGSCLF GAISRSLFKK LPIPYTVVLL ILGAILGVV ASNVPLVEEH TRDVAHMDPH VLLQIFLPVL IFESAFAMDV HTFMRSFSQV CILALFGLVV ASVLTAVLAM N LFNYNWNF ...String:
GSSSGGSGHT PTTQATHADD HDLTTHNGTE EHDDGHDDGH DDLHAHAPKV IVFISGSCLF GAISRSLFKK LPIPYTVVLL ILGAILGVV ASNVPLVEEH TRDVAHMDPH VLLQIFLPVL IFESAFAMDV HTFMRSFSQV CILALFGLVV ASVLTAVLAM N LFNYNWNF SEAMMFGAIM SATDPVAVVA LLKDLGASKQ LGTIIEGESL LNDGCAIVIF NVFMKMVFFP QLTSTVGQNV LY FLQVAVA GPLWGYAVAK VTVFFLSHIF NDALVEITIT LAATYLTYYI GDIWLEVSGV LAVVVLGLIV NAEKTSISPE VEV FLHRFW EMLAYLANTL IFMMVGVVVT QKALVAVDKM DWFYLIILYL AITIIRGMVI SLFSPILSRI GYGLTWRNAV IMTW GGLRG AVGLALALVV ENLAGNDVIG SKFLFHTAGI VVLTLVINAT TIQTLLRILG MSDISIPKRL AMAGAVRRIH EGQNR TLNM LKSDRFLADA DWDIATAACE ISDPYSALSD DENAPADELT LGERKSVCPG CKAMVPNEPS PREFADMMEE ARLRML KAE KISYWKQFEH GMLAREALRL LVQHAEVAAD EKDQFILVDD LKKSWQIKGI YPWLKRKLED LISEKKIAAI PMPKYKL GK LMYKICHHMA FEVTINIAIV LNIVPIIMEF VVQDKMASVS TMAAPGSTVS SEPSSLQKIE DALRISNYVF FVIYAIEA I VKILGLGRHY IVSHWNKFDA FILVVALVDI IIAETLLKGS ITINLSSIKV VKLFRLLRGL RMLRLTKALI PKLILVVNG KINNQLSLGY DVGKGYIIGE EEVGKIIDRM VDNKKILREL KHISETGRLQ VVKELGLLQR EHPGIAVSVK TRQAIRTILN HSRETIHEL QGAGLLDEME AHKLELTVEI KMKRLMNAPS SIPPPPPENL LKNVSWLAGD MKLIDFIKAR ASLLHFDYGE V IVREGDES DGLFLIVSGL VKLYGKSAFL DHDNPPVTAG SEENEVFEDY LTVGNVIGEM GVLTKKPRNA TVTCETTVQV YF ITAEDMN IAIDTFTLYP SLEYRLWRVV AIRIATPLIM EQMAFQGWTQ EKVKLHLERG YLVDLAESHF QFNIDATLED VIL INGTAY NAHTREEIRS PCLISRTVHK LTFQYTATEE PRLFVVRNAE YNGPILDGRL DVDSKRSLIS ITEISSNMCL KHAA ELRQK NSKVMLSRKS SGAAAKEEED CIPNTSDVEQ AAGVSPSVPT KTTPKPKSFL PSLGLSMSKE RVNGEAVEES PVKTK QGEE TPETEEGAAP RVNVASNSLE VLFQ

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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225150
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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