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- EMDB-19995: Non-uniform refinement of the CryoEM structure of DeCLIC nanodisc... -

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Basic information

Entry
Database: EMDB / ID: EMD-19995
TitleNon-uniform refinement of the CryoEM structure of DeCLIC nanodisc with 10mM EDTA in asym state
Map data
Sample
  • Complex: DeCLIC in 10mM calcium
    • Protein or peptide: Neur_chan_LBD domain-containing protein
  • Ligand: N-OCTANE
  • Ligand: DECANE
  • Ligand: TETRADECANE
KeywordsIon channel / TRANSLOCASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsFan C / Howard RJ / Lindahl E
Funding support1 items
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, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19995.png

Downloads & links

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Map

FileDownload / File: emd_19995.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 270.848 Å		0.85 Å/pix.
x 320 pix.
= 270.848 Å		0.85 Å/pix.
x 320 pix.
= 270.848 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.1343403 - 2.4595084
Average (Standard dev.)0.0022130238 (±0.07034735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 270.84802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19995_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19995_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : DeCLIC in 10mM calcium

EntireName: DeCLIC in 10mM calcium
Components
  • Complex: DeCLIC in 10mM calcium
    • Protein or peptide: Neur_chan_LBD domain-containing protein
  • Ligand: N-OCTANE
  • Ligand: DECANE
  • Ligand: TETRADECANE

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Supramolecule #1: DeCLIC in 10mM calcium

SupramoleculeName: DeCLIC in 10mM calcium / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Desulfofustis sp. PB-SRB1 (bacteria)

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Macromolecule #1: Neur_chan_LBD domain-containing protein

MacromoleculeName: Neur_chan_LBD domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Desulfofustis sp. PB-SRB1 (bacteria)
Molecular weightTheoretical: 71.733992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHNLQQLLPT RSLIWIFSFL TSISIWCTVA HAETEGRVQH FTGYIEDGRG IFYSLPDMKQ GDIIYASMQN TGGNLDPLVG IMAEEIDPA VSLGQVLEKA LASENDLISE LTAVADRIFL GWDDDGGKGY SASLEFTIPR DGTYHIFAGS TITNQRLDKF Q PTYTTGSF ...String:
MHNLQQLLPT RSLIWIFSFL TSISIWCTVA HAETEGRVQH FTGYIEDGRG IFYSLPDMKQ GDIIYASMQN TGGNLDPLVG IMAEEIDPA VSLGQVLEKA LASENDLISE LTAVADRIFL GWDDDGGKGY SASLEFTIPR DGTYHIFAGS TITNQRLDKF Q PTYTTGSF QLILGLNAPQ VISGEGEPEG EVFASLASLE IKPEAHVQEL EIRLDKDTRY LTQHTRNLQP GDTFHALVEP IG EAPLPRL RLTDSGGKPL AFGLIDQPGE SVELNYTCDQ DICELVVHVD GTDGQKDSGE AVYRLLVGIN APNLRESGQT PVG SSVFLE SDLVTVGLAV DQIVGVDQRS ENFSVVGTLK LSWHDPKLGF SPDQCGCTVK SFEDASIRAV AGEINLPLPS FSFY NQQGN RWSQNQVIFV TPDGRASYFE RFTVTLQAPD FDFLAYPFDR QKFSIKVDLA VPTNMFIFNE IERFQQVVGD QLGEE EWVV TSYSQEITEV PFERGSTNSR FTTTLLVKRN LEYYILRIFV PLFLIISVSW VIFFLKDYGR QLEVASGNLL VFVAFN FTI SGDLPRLGYL TVLDRFMIVS FCLTAIVVLI SVCQKRLGAV GKQAVAAQID TWVLVIYPLV YSLYIIWVYL RFFTDHI GW

UniProtKB: Uncharacterized protein

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Macromolecule #2: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 2 / Number of copies: 15 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #3: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 3 / Number of copies: 15 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #4: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 4 / Number of copies: 5 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 302612
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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