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- EMDB-34822: Human Cx36/GJD2 (BRIL-fused mutant) gap junction channel in soybe... -

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Basic information

Entry
Database: EMDB / ID: EMD-34822
TitleHuman Cx36/GJD2 (BRIL-fused mutant) gap junction channel in soybean lipids
Map datacoulomb density map of Cx36-BRIL gap junction channel in lipid nanodiscs (soybean lipids).
Sample
  • Complex: Cx36-BRIL
Keywordsconnexin 36 / Cx36 / Gap Junction Channel / BRIL / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCho HJ / Lee SN / Jeong H / Ryu B / Lee HJ / Woo JS / Lee HH
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2022R1A2B5B02002529 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1C1B6004447 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel.
Authors: Seu-Na Lee / Hwa-Jin Cho / Hyeongseop Jeong / Bumhan Ryu / Hyuk-Joon Lee / Minsoo Kim / Jejoong Yoo / Jae-Sung Woo / Hyung Ho Lee /
Abstract: Connexin 36 (Cx36) is responsible for signal transmission in electrical synapses by forming interneuronal gap junctions. Despite the critical role of Cx36 in normal brain function, the molecular ...Connexin 36 (Cx36) is responsible for signal transmission in electrical synapses by forming interneuronal gap junctions. Despite the critical role of Cx36 in normal brain function, the molecular architecture of the Cx36 gap junction channel (GJC) is unknown. Here, we determine cryo-electron microscopy structures of Cx36 GJC at 2.2-3.6 Å resolutions, revealing a dynamic equilibrium between its closed and open states. In the closed state, channel pores are obstructed by lipids, while N-terminal helices (NTHs) are excluded from the pore. In the open state with pore-lining NTHs, the pore is more acidic than those in Cx26 and Cx46/50 GJCs, explaining its strong cation selectivity. The conformational change during channel opening also includes the α-to-π-helix transition of the first transmembrane helix, which weakens the protomer-protomer interaction. Our structural analyses provide high resolution information on the conformational flexibility of Cx36 GJC and suggest a potential role of lipids in the channel gating.
History
DepositionNov 21, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34822.png

Downloads & links

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Map

FileDownload / File: emd_34822.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcoulomb density map of Cx36-BRIL gap junction channel in lipid nanodiscs (soybean lipids).
Voxel sizeX=Y=Z: 0.6747 Å
Density
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-1.444248 - 2.7474816
Average (Standard dev.)0.01360105 (±0.092670366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 345.4464 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A of Cx36-BRIL gap junction channel...

Fileemd_34822_half_map_1.map
Annotationhalf map A of Cx36-BRIL gap junction channel in lipid nanodiscs (soybean lipids).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of Cx36-BRIL gap junction channel...

Fileemd_34822_half_map_2.map
Annotationhalf map B of Cx36-BRIL gap junction channel in lipid nanodiscs (soybean lipids).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cx36-BRIL

EntireName: Cx36-BRIL
Components
  • Complex: Cx36-BRIL

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Supramolecule #1: Cx36-BRIL

SupramoleculeName: Cx36-BRIL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10611

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