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- PDB-9ev1: 3DFlex refinement of the CryoEM structure of DeCLIC nanodisc with... -

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Basic information

Entry
Database: PDB / ID: 9ev1
Title3DFlex refinement of the CryoEM structure of DeCLIC nanodisc with 10mM EDTA in sym-like state
ComponentsNeur_chan_LBD domain-containing protein
KeywordsTRANSLOCASE / Ion channel
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: 2.63 Å
AuthorsFan, C. / Howard, R.J. / Lindahl, E.
Funding support1items
OrganizationGrant numberCountry
Swedish Research Council
CitationJournal: J Struct Biol X / Year: 2025
Title: Calcium stabilizes the flexible N-terminal domain of the bacterial ion channel DeCLIC.
Authors: Chen Fan / Marie Lycksell / Yuxuan Zhuang / Rebecca J Howard / Erik Lindahl /
Abstract: Pentameric ligand-gated ion channels (pLGICs) are responsible for the rapid conversion of chemical to electrical signals. In addition to the canonical extracellular and transmembrane domains, some ...Pentameric ligand-gated ion channels (pLGICs) are responsible for the rapid conversion of chemical to electrical signals. In addition to the canonical extracellular and transmembrane domains, some prokaryotic pLGICs contain an N-terminal domain (NTD) of unclear structure and function. In one such case, the calcium-sensitive channel DeCLIC, the NTD appears to accelerate gating; however, its evident flexibility has posed a challenge to model building, and its role in calcium sensitivity is unclear. Here we report cryo-EM structures of DeCLIC in circularized lipid nanodiscs, achieving the highest resolution reported so far, and enabling definition of calcium-binding sites in both the N-terminal and canonical extracellular domains. In addition to the symmetric state, calcium depletion promoted an asymmetric conformation of the NTD, offering a structural rationale for small-angle scattering results. Behavior of these structures in molecular dynamics simulations demonstrated calcium stabilization of the NTD. These features of DeCLIC offer a model system for ion-channel modulation by a flexible accessory domain, potentially conserved in structurally homologous systems across evolution.
History
DepositionMar 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neur_chan_LBD domain-containing protein
B: Neur_chan_LBD domain-containing protein
C: Neur_chan_LBD domain-containing protein
D: Neur_chan_LBD domain-containing protein
E: Neur_chan_LBD domain-containing protein


Theoretical massNumber of molelcules
Total (without water)358,6705
Polymers358,6705
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Neur_chan_LBD domain-containing protein / Ligand-gated ion channel DeCLIC


Mass: 71733.992 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfofustis sp. PB-SRB1 (bacteria) / Gene: 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: DeCLIC in 10mM calcium / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Desulfofustis sp. PB-SRB1 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategoryDetails
8PHENIXmodel refinement
13cryoSPARC3D reconstruction3DFlex
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 350000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00224200
ELECTRON MICROSCOPYf_angle_d0.41332935
ELECTRON MICROSCOPYf_dihedral_angle_d8.6538720
ELECTRON MICROSCOPYf_chiral_restr0.043735
ELECTRON MICROSCOPYf_plane_restr0.0034285

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