9YDF | pdb_00009ydf

Structure of the cyclic nucleotide binding domain of SLC9C1

• PDB DOI: https://doi.org/10.2210/pdb9YDF/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-22 Released: 2025-11-12 
• Deposition Author(s): Lyu, C., Dong, A., Chandrasekaran, R., Mamai, A., Arrowsmith, C.H., Edwards, A.M., Burgess-Brown, N., Tredup, C., Harding, R.J., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.237 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

Literature

Structure of the cyclic nucleotide binding domain of SLC9C1

Lyu, C., Dong, A., Chandrasekaran, R., Mamai, A., Arrowsmith, C.H., Edwards, A.M., Burgess-Brown, N., Tredup, C., Harding, R.J., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.11 kDa 
• Atom Count: 1,043 
• Modeled Residue Count: 131 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 9 member C1	A	173	Homo sapiens	Mutation(s): 0  Gene Names: SLC9C1, SLC9A10
UniProt & NIH Common Fund Data Resources
Find proteins for Q4G0N8 (Homo sapiens) Explore Q4G0N8  Go to UniProtKB:  Q4G0N8
PHAROS:  Q4G0N8 GTEx:  ENSG00000172139

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.237 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.788	α = 90
b = 45.788	β = 90
c = 276.932	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Lyu, C., Dong, A., Chandrasekaran, R., Mamai, A., Arrowsmith, C.H., Edwards, A.M., Burgess-Brown, N., Tredup, C., Harding, R.J., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release