9FTG | pdb_00009ftg

Closed conformation of the pentameric ligand-gated ion channel, DeCLIC at pH 5 with 10 mM Ca2+

• PDB DOI: https://doi.org/10.2210/pdb9FTG/pdb
• EM Map EMD-50744: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Desulfofustis sp. PB-SRB1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-24 Released: 2024-09-11 
• Deposition Author(s): Rovsnik, U., Anden, O., Lycksell, M., Delarue, M., Howard, R.J., Lindahl, E.
• Funding Organization(s): Knut and Alice Wallenberg Foundation, Swedish Research Council

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural characterization of pH-modulated closed and open states in a pentameric ligand-gated ion channel

Rovsnik, U., Anden, O., Lycksell, M., Delarue, M., Howard, R.J., Lindahl, E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 339.66 kDa 
• Atom Count: 21,205 
• Modeled Residue Count: 2,795 
• Deposited Residue Count: 3,045 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein	A, B, C [auth D], D [auth E], E [auth C]	609	Desulfofustis sp. PB-SRB1	Mutation(s): 0  Gene Names: JKP90_15375, N839_03575

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	F [auth A], G [auth B], H [auth D], I [auth E], J [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Rovsnik, U., Anden, O., Lycksell, M., Delarue, M., Howard, R.J., Lindahl, E.

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Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	--
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-02
  Changes: Data collection