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- PDB-8xpq: Structure of the sea urchin spSLC9C1 in state-2 w/o cAMP dimer -

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Basic information

Entry
Database: PDB / ID: 8xpq
TitleStructure of the sea urchin spSLC9C1 in state-2 w/o cAMP dimer
ComponentsSperm-specific sodium proton exchanger
KeywordsTRANSPORT PROTEIN / Transporter / Sodium-hydrogen exchanger
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 / regulation of intracellular pH ...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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsQu, H. / Zheng, X.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jul 17, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sperm-specific sodium proton exchanger
B: Sperm-specific sodium proton exchanger


Theoretical massNumber of molelcules
Total (without water)289,9002
Polymers289,9002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sperm-specific sodium proton exchanger


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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: dimer of sea urchin solute carrier 9C1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 441138 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616248
ELECTRON MICROSCOPYf_angle_d0.77422054
ELECTRON MICROSCOPYf_dihedral_angle_d13.2365838
ELECTRON MICROSCOPYf_chiral_restr0.052658
ELECTRON MICROSCOPYf_plane_restr0.0072752

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