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- PDB-9ftj: Closed and disordered conformation of the pentameric ligand-gated... -

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Basic information

Entry
Database: PDB / ID: 9ftj
TitleClosed and disordered conformation of the pentameric ligand-gated ion channel, DeCLIC at pH 5 with 10mM EDTA
ComponentsNeurotransmitter-gated ion-channel ligand-binding domain-containing protein
KeywordsMEMBRANE PROTEIN / Pentameric ligand-gated ion channel / pLGIC
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / membrane
Similarity search - Function
Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesDesulfofustis sp. PB-SRB1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsRovsnik, U. / Anden, O. / Lycksell, M. / Delarue, M. / Howard, R.J. / Lindahl, E.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Structural characterization of pH-modulated closed and open states in a pentameric ligand-gated ion channel
Authors: Rovsnik, U. / Anden, O. / Lycksell, M. / Delarue, M. / Howard, R.J. / Lindahl, E.
History
DepositionJun 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
B: Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
C: Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
D: Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
E: Neurotransmitter-gated ion-channel ligand-binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)339,4575
Polymers339,4575
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein


Mass: 67891.492 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfofustis sp. PB-SRB1 (bacteria) / Gene: JKP90_15375, N839_03575 / Production host: Escherichia coli (E. coli) / References: UniProt: V4JF97
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pentameric ligan-gated ion channel DeCLIC / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Desulfacinum sp. (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 5
Buffer componentConc.: 10 mM / Name: EDTA
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: LAB6 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1600 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 43.9 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 26757

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4CTF correction
8PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3500000
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00712375
ELECTRON MICROSCOPYf_angle_d0.6416930
ELECTRON MICROSCOPYf_dihedral_angle_d4.6541685
ELECTRON MICROSCOPYf_chiral_restr0.0451995
ELECTRON MICROSCOPYf_plane_restr0.0052125

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