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- EMDB-12677: GLIC, pentameric ligand-gated ion channel, pH 5, state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-12677
TitleGLIC, pentameric ligand-gated ion channel, pH 5, state 2
Map dataRefine 3D map, pH 5 state 2
Sample
  • Complex: Pentameric ion channel
    • Protein or peptide: Proton-gated channel
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / transmembrane transporter complex / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain superfamily / 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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
Methodsingle particle reconstruction / cryo EM
AuthorsRovsnik U / Zhuang Y / Forsberg BO / Carroni M / Yvonnesdotter L / Howard RJ / Lindahl E
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Life Sci Alliance / Year: 2021
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
DepositionMar 26, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJan 26, 2022-
Current statusJan 26, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12677.png

Downloads & links

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Map

FileDownload / File: emd_12677.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefine 3D map, pH 5 state 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.008009007 - 0.02375254
Average (Standard dev.)0.0005363919 (±0.0018726662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z209.920209.920209.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0080.0240.001

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Supplemental data

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Mask #1

Fileemd_12677_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed map, pH 5, state 2

Fileemd_12677_additional_1.map
AnnotationPostprocessed map, pH 5, state 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2, pH 5, state 2

Fileemd_12677_half_map_1.map
AnnotationHalf map 2, pH 5, state 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1, pH 5, state 2

Fileemd_12677_half_map_2.map
AnnotationHalf map 1, pH 5, state 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pentameric ion channel

EntireName: Pentameric ion channel
Components
  • Complex: Pentameric ion channel
    • Protein or peptide: Proton-gated channel

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Supramolecule #1: Pentameric ion channel

SupramoleculeName: Pentameric ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Gloeobacter violaceus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Proton-gated channel

MacromoleculeName: Proton-gated channel / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: AQDMVSPPPP IADEPLTVNT GIYLIECYSL DDKAETFKVN AFLSLSWKDR RLAFDPVRSG VRVKTYEPEA IWIPEIRFVN VENARDADVV DISVSPDGTV QYLERFSARV LSPLDFRRYP FDSQTLHIYL IVRSVDTRNI VLAVDLEKVG KNDDVFLTGW DIESFTAVVK ...String:
AQDMVSPPPP IADEPLTVNT GIYLIECYSL DDKAETFKVN AFLSLSWKDR RLAFDPVRSG VRVKTYEPEA IWIPEIRFVN VENARDADVV DISVSPDGTV QYLERFSARV LSPLDFRRYP FDSQTLHIYL IVRSVDTRNI VLAVDLEKVG KNDDVFLTGW DIESFTAVVK PANFALEDRL ESKLDYQLRI SRQYFSYIPN IILPMLFILF ISWTAFWSTS YEANVTLVVS TLIAHIAFNI LVETNLPKTP YMTYTGAIIF MIYLFYFVAV IEVTVQHYLK VESQPARAAS ITRASRIAFP VVFLLANIIL AFLFFGF

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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

Concentration3 mg/mL
BufferpH: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 18000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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