8XQ5 | pdb_00008xq5

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

PDB DOI: https://doi.org/10.2210/pdb8XQ5/pdb
EM Map EMD-38566: EMDB EMDataResource

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

Deposited: 2024-01-04 Released: 2025-01-15
Deposition Author(s): Qu, H., Zheng, X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8XQ5

This is version 1.1 of the entry. See complete history.

Literature

Structures of a sperm-specific sodium-hydrogen exchanger

Qu, H., Zheng, X.

To be published.

Macromolecule Content

Total Structure Weight: 289.9 kDa
Atom Count: 15,128
Modeled Residue Count: 1,966
Deposited Residue Count: 2,616
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3RL54
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.15 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release
Version 1.1: 2025-07-02
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.