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- PDB-9evb: Non-uniform refinement of the CryoEM structure of DeCLIC nanodisc... -

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Basic information

Entry
Database: PDB / ID: 9evb
TitleNon-uniform 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
TETRADECANE / DECANE / N-OCTANE / Uncharacterized protein
Similarity search - Component
Biological speciesDesulfofustis sp. PB-SRB1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsFan, C. / Howard, R.J. / Lindahl, E.
Funding support1items
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, R.J. / Lindahl, E.
History
DepositionMar 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Category: em_admin / em_software / 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,51040
Polymers358,6705
Non-polymers4,84035
Water3,693205
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
#2: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H30 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: #1 / 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 softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 395520 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00624390
ELECTRON MICROSCOPYf_angle_d1.03533060
ELECTRON MICROSCOPYf_dihedral_angle_d11.7138870
ELECTRON MICROSCOPYf_chiral_restr0.0633715
ELECTRON MICROSCOPYf_plane_restr0.0114275

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