+Open data
-Basic information
Entry | Database: PDB / ID: 8xpq | ||||||
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Title | Structure of the sea urchin spSLC9C1 in state-2 w/o cAMP dimer | ||||||
Components | Sperm-specific sodium proton exchanger | ||||||
Keywords | TRANSPORT PROTEIN / Transporter / Sodium-hydrogen exchanger | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Qu, H. / Zheng, X. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xpq.cif.gz | 413.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xpq.ent.gz | 321.9 KB | Display | PDB format |
PDBx/mmJSON format | 8xpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xpq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8xpq_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8xpq_validation.xml.gz | 60.2 KB | Display | |
Data in CIF | 8xpq_validation.cif.gz | 89.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/8xpq ftp://data.pdbj.org/pub/pdb/validation_reports/xp/8xpq | HTTPS FTP |
-Related structure data
Related structure data | 38559MC 8xq4C 8xq7C 8xq8C 8xq9C 8xqaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 144950.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Strongylocentrotus purpuratus (purple sea urchin) Gene: spSLC9C1 / Production host: Homo sapiens (human) / References: UniProt: A3RL54 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: dimer of sea urchin solute carrier 9C1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Strongylocentrotus purpuratus (purple sea urchin) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 441138 / Symmetry type: POINT | ||||||||||||||||||||||||
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