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- EMDB-33274: Human Cx36/GJD2 (N-terminal deletion mutant) gap junction channel... -

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Basic information

Entry
Database: EMDB / ID: EMD-33274
TitleHuman Cx36/GJD2 (N-terminal deletion mutant) gap junction channel in soybean lipids (D6 symmetry)
Map datasharpened map
Sample
  • Complex: Cx36-delN8
    • Protein or peptide: Gap junction delta-2 protein
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
KeywordsConnexin 36 / Cx36 / Gap Junction Channel / GJD2 / MEMBRANE PROTEIN
Function / homology
Function and homology information


Electric Transmission Across Gap Junctions / connexin complex / Gap junction assembly / gap junction channel activity / neuronal action potential / visual perception / cell-cell signaling / chemical synaptic transmission / synapse / plasma membrane
Similarity search - Function
Gap junction delta-2 protein (Cx36) / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain
Similarity search - Domain/homology
Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLee SN / Cho HJ / Jeong H / Ryu B / Lee HJ / Lee HH / Woo JS
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1C1B6004447 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1A2B5B02002529 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
DepositionApr 21, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33274.png

Downloads & links

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Map

FileDownload / File: emd_33274.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 0.8415 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.3478845 - 1.8842142
Average (Standard dev.)0.00038980794 (±0.045015268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.94 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_33274_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_33274_half_map_2.map
Annotationhalf map A
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-delN8

EntireName: Cx36-delN8
Components
  • Complex: Cx36-delN8
    • Protein or peptide: Gap junction delta-2 protein
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Cx36-delN8

SupramoleculeName: Cx36-delN8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gap junction delta-2 protein

MacromoleculeName: Gap junction delta-2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.584242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRLLEAAVQQ HSTMIGRILL TVVVIFRILI VAIVGETVYD DEQTMFVCNT LQPGCNQACY DRAFPISHIR YWVFQIIMVC TPSLCFITY SVHQSAKQRE RRYSTVFLAL DRDPPESIGG PGGTGGGGSG GGKREDKKLQ NAIVNGVLQN TENTSKETEP D CLEVKELT ...String:
MRLLEAAVQQ HSTMIGRILL TVVVIFRILI VAIVGETVYD DEQTMFVCNT LQPGCNQACY DRAFPISHIR YWVFQIIMVC TPSLCFITY SVHQSAKQRE RRYSTVFLAL DRDPPESIGG PGGTGGGGSG GGKREDKKLQ NAIVNGVLQN TENTSKETEP D CLEVKELT PHPSGLRTAS KSKLRRQEGI SRFYIIQVVF RNALEIGFLV GQYFLYGFSV PGLYECNRYP CIKEVECYVS RP TEKTVFL VFMFAVSGIC VVLNLAELNH LGWRKIKLAV RGAQAKRKSI YEIRNKDLPR VSVPNFGRTQ SSDSAYVSRG DML EVLFQ

UniProtKB: Gap junction delta-2 protein

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Macromolecule #2: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 84 / Formula: MC3
Molecular weightTheoretical: 677.933 Da
Chemical component information

ChemComp-MC3:
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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: 2.4 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 460806

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