8U7D | pdb_00008u7d

R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed state

PDB DOI: https://doi.org/10.2210/pdb8U7D/pdb
EM Map EMD-41979: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Strongylocentrotus purpuratus
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-09-15 Released: 2025-03-26
Deposition Author(s): Chowdhury, S., Pal, K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8U7D

This is version 1.0 of the entry. See complete history.

Literature

R399A mutant of sea urchin SLC9C1 at pH 6 in Na+ - Relaxed form

Chowdhury, S., Pal, K.

To be published.

Macromolecule Content

Total Structure Weight: 300.5 kDa
Atom Count: 14,924
Modeled Residue Count: 1,846
Deposited Residue Count: 2,650
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	1,325	Strongylocentrotus purpuratus	Mutation(s): 1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AJP (Subject of Investigation/LOI) Query on AJP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], I [auth B]	Digitonin C₅₆ H₉₂ O₂₉ UVYVLBIGDKGWPX-KUAJCENISA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]
POV (Subject of Investigation/LOI) Query on POV Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM145719

Revision History (Full details and data files)

Version 1.0: 2025-03-26
Type: Initial release

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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.