+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38559 | |||||||||
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Title | Structure of the sea urchin spSLC9C1 in state-2 w/o cAMP dimer | |||||||||
Map data | map of 9C1 apo state-2 dimer | |||||||||
Sample |
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Keywords | Transporter / Sodium-hydrogen exchanger / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information potassium:proton antiporter activity / sperm head / 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 ...potassium:proton antiporter activity / sperm head / 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: 3.1 Å | |||||||||
Authors | Qu H / Zheng X | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38559.map.gz | 57.2 MB | EMDB map data format | |
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Header (meta data) | emd-38559-v30.xml emd-38559.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_38559.png | 111.5 KB | ||
Filedesc metadata | emd-38559.cif.gz | 5.8 KB | ||
Others | emd_38559_half_map_1.map.gz emd_38559_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38559 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38559 | HTTPS FTP |
-Validation report
Summary document | emd_38559_validation.pdf.gz | 662.2 KB | Display | EMDB validaton report |
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Full document | emd_38559_full_validation.pdf.gz | 661.8 KB | Display | |
Data in XML | emd_38559_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_38559_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38559 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38559 | HTTPS FTP |
-Related structure data
Related structure data | 8xpqMC 8xq4C 8xq7C 8xq8C 8xq9C 8xqaC M: atomic model generated by this map 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_38559.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | map of 9C1 apo state-2 dimer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B of 9C1 apo state-2 dimer
File | emd_38559_half_map_1.map | ||||||||||||
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Annotation | half map B of 9C1 apo state-2 dimer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A of 9C1 apo state-2 dimer
File | emd_38559_half_map_2.map | ||||||||||||
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Annotation | half map A of 9C1 apo state-2 dimer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : dimer of sea urchin solute carrier 9C1
Entire | Name: dimer of sea urchin solute carrier 9C1 |
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Components |
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-Supramolecule #1: dimer of sea urchin solute carrier 9C1
Supramolecule | Name: dimer of sea urchin solute carrier 9C1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Strongylocentrotus purpuratus (purple sea urchin) |
-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: Strongylocentrotus purpuratus (purple sea urchin) |
Molecular weight | Theoretical: 144.950125 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 441138 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |