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- EMDB-19994: Non-uniform refinement of the CryoEM structure of DeCLIC nanodisc... -

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Basic information

Entry
Database: EMDB / ID: EMD-19994
TitleNon-uniform refinement of the CryoEM structure of DeCLIC nanodisc with 10mM calcium
Map data
Sample
  • Complex: DeCLIC in 10mM calcium
    • Protein or peptide: Neur_chan_LBD domain-containing protein
  • Ligand: CALCIUM ION
  • Ligand: N-OCTANE
  • Ligand: DODECANE
  • Ligand: DECANE
  • Ligand: TETRADECANE
  • Ligand: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: water
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: 2.06 Å
AuthorsFan C / Howard RJ / Lindahl E
Funding support1 items
OrganizationGrant numberCountry
Swedish Research Council
CitationJournal: To Be Published
Title: Calcium stabilization of a flexible N-terminal domain in a pentameric ligand-gated ion channel
Authors: Fan C / Howard RJ / Lindahl E
History
DepositionMar 28, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19994.png

Downloads & links

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Map

FileDownload / File: emd_19994.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 380 pix.
= 321.632 Å		0.85 Å/pix.
x 380 pix.
= 321.632 Å		0.85 Å/pix.
x 380 pix.
= 321.632 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-4.435542 - 6.8489966
Average (Standard dev.)0.00073828275 (±0.097784065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 321.63202 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19994_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19994_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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: CALCIUM ION
  • Ligand: N-OCTANE
  • Ligand: DODECANE
  • Ligand: DECANE
  • Ligand: TETRADECANE
  • Ligand: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: water

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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: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 10 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 3 / Number of copies: 10 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #4: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 4 / Number of copies: 10 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #5: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 5 / Number of copies: 5 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #6: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 6 / Number of copies: 5 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #7: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 7 / Number of copies: 5 / Formula: PX6
Molecular weightTheoretical: 647.883 Da
Chemical component information

ChemComp-PX6:
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 215 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 894494
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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