8XQA | pdb_00008xqa

Structure of the sea urchin spSLC9C1 in state-3 w/ cAMP dimer

• PDB DOI: https://doi.org/10.2210/pdb8XQA/pdb
• EM Map EMD-38571: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Strongylocentrotus purpuratus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2024-01-04 Released: 2024-07-17 
• Deposition Author(s): Qu, H., Zheng, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of a sperm-specific sodium-hydrogen exchanger.

Qu, H., Zhen, Y., Xu, M., Huang, Y., Wang, Y., Ji, G., Zhang, Y., Li, H., Dong, Z., Zheng, X.

(2024) Cell Insight 3: 100177-100177

• PubMed: 38957574 
• DOI: https://doi.org/10.1016/j.cellin.2024.100177
• Primary Citation of Related Structures:  
  8XPQ, 8XQ4, 8XQ7, 8XQ8, 8XQ9, 8XQA

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Organizational Affiliation: 
• Academy of Medical Sciences, Tianjian Laboratory of Advanced Biomedical Sciences, State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, 450001, China.
State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing, 100084, China.
Beijing Frontier Research Center for Biological Structure and Beijing Advanced Innovation Center for Structural Biology, Beijing, 100084, China.
Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Beijing, 100048, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 289.9 kDa 
• Atom Count: 10,602 
• Modeled Residue Count: 1,356 
• Deposited Residue Count: 2,616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sperm-specific sodium proton exchanger	A, B	1,308	Strongylocentrotus purpuratus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A3RL54 (Strongylocentrotus purpuratus) Explore A3RL54  Go to UniProtKB:  A3RL54

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.54 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Qu, H., Zheng, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371292

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2025-06-18
  Changes: Data collection, Structure summary