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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11209 | |||||||||
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Title | GLIC pentameric ligand-gated ion channel, pH 3 | |||||||||
![]() | GLIC, pentameric ligand-gated ion channel, pH 3, sharpened map | |||||||||
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![]() | GLIC / pentameric ligand-gated ion channel / cryoem / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Rovsnik U / Zhuang Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations. Authors: Urška Rovšnik / Yuxuan Zhuang / Björn O Forsberg / Marta Carroni / Linnea Yvonnesdotter / Rebecca J Howard / Erik Lindahl / ![]() ![]() Abstract: Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological characterization of these receptor proteins relies on high- ...Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological characterization of these receptor proteins relies on high-quality structures in multiple, subtly distinct functional states. However, structural data in this family remain limited, particularly for resting and intermediate states on the activation pathway. Here, we report cryo-electron microscopy (cryo-EM) structures of the proton-activated ligand-gated ion channel (GLIC) under three pH conditions. Decreased pH was associated with improved resolution and side chain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the β1-β2 and M2-M3 loops. Molecular dynamics simulations substantiated flexibility in the closed-channel extracellular domains relative to the transmembrane ones and supported electrostatic remodeling around E35 and E243 in proton-induced gating. Exploration of secondary cryo-EM classes further indicated a low-pH population with an expanded pore. These results allow us to define distinct protonation and activation steps in pH-stimulated conformational cycling in GLIC, including interfacial rearrangements largely conserved in the pentameric channel family. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.5 KB 19.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 150.3 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() ![]() | 49.6 MB 49.8 MB 49.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 681.6 KB | Display | ![]() |
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Full document | ![]() | 681.2 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zgkMC ![]() 6zgdC ![]() 6zgjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | GLIC, pentameric ligand-gated ion channel, pH 3, sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: GLIC, pentameric ligand-gated ion channel, pH 3, unsharpened map
File | emd_11209_additional_1.map | ||||||||||||
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Annotation | GLIC, pentameric ligand-gated ion channel, pH 3, unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: GLIC, pentameric ligand-gated ion channel, pH 3, half map 1
File | emd_11209_half_map_1.map | ||||||||||||
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Annotation | GLIC, pentameric ligand-gated ion channel, pH 3, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: GLIC, pentameric ligand-gated ion channel, pH 3, half map 2
File | emd_11209_half_map_2.map | ||||||||||||
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Annotation | GLIC, pentameric ligand-gated ion channel, pH 3, half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Pentameric ion channel
Entire | Name: Pentameric ion channel |
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Components |
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-Supramolecule #1: Pentameric ion channel
Supramolecule | Name: Pentameric ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: Proton-gated ion channel
Macromolecule | Name: Proton-gated ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 29082 / PCC 7421 |
Molecular weight | Theoretical: 36.29175 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AQDMVSPPPP IADEPLTVNT GIYLIECYSL DDKAETFKVN AFLSLSWKDR RLAFDPVRSG VRVKTYEPEA IWIPEIRFVN VENARDADV VDISVSPDGT VQYLERFSAR VLSPLDFRRY PFDSQTLHIY LIVRSVDTRN IVLAVDLEKV GKNDDVFLTG W DIESFTAV ...String: AQDMVSPPPP IADEPLTVNT GIYLIECYSL DDKAETFKVN AFLSLSWKDR RLAFDPVRSG VRVKTYEPEA IWIPEIRFVN VENARDADV VDISVSPDGT VQYLERFSAR VLSPLDFRRY PFDSQTLHIY LIVRSVDTRN IVLAVDLEKV GKNDDVFLTG W DIESFTAV VKPANFALED RLESKLDYQL RISRQYFSYI PNIILPMLFI LFISWTAFWS TSYEANVTLV VSTLIAHIAF NI LVETNLP KTPYMTYTGA IIFMIYLFYF VAVIEVTVQH YLKVESQPAR AASITRASRI AFPVVFLLAN IILAFLFFGF UniProtKB: Proton-gated ion channel |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 1.5 s force -1. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 6000 / Average exposure time: 6.0 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 0.0028 µm / Calibrated defocus min: 0.0009000000000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |