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- EMDB-33254: Human Cx36/GJD2 (N-terminal deletion BRIL-fused mutant) gap junct... -

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Basic information

Entry
Database: EMDB / ID: EMD-33254
TitleHuman Cx36/GJD2 (N-terminal deletion BRIL-fused mutant) gap junction channel in soybean lipids (D6 symmetry)
Map datasharpened EM map
Sample
  • Complex: Cx36-BRIL-DelN16
    • Protein or peptide: Gap junction delta-2 protein,Soluble cytochrome b562
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
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 / electron transfer activity / periplasmic space ...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 / electron transfer activity / periplasmic space / iron ion binding / synapse / heme binding / 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 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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Gap junction delta-2 protein
Similarity search - Component
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
DepositionApr 19, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33254.png

Downloads & links

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Map

FileDownload / File: emd_33254.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened EM map
Voxel sizeX=Y=Z: 0.6747 Å
Density
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-1.547638 - 2.7730715
Average (Standard dev.)0.00023012361 (±0.0586051)
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 for FSC

Fileemd_33254_half_map_1.map
Annotationhalf map A for FSC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B for FSC

Fileemd_33254_half_map_2.map
Annotationhalf map B for FSC
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-DelN16

EntireName: Cx36-BRIL-DelN16
Components
  • Complex: Cx36-BRIL-DelN16
    • Protein or peptide: Gap junction delta-2 protein,Soluble cytochrome b562
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Cx36-BRIL-DelN16

SupramoleculeName: Cx36-BRIL-DelN16 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gap junction delta-2 protein,Soluble cytochrome b562

MacromoleculeName: Gap junction delta-2 protein,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1
Details: The chimeric protein of Cx36 (UNP residue 1), Cx36 (UNP residues 17-108), BRIL (UNP residues 23-123 with mutation M29W, H124I, R128L), Cx36 (UNP residues 188-321), linker and tags
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.288258 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQHSTMIGRI LLTVVVIFRI LIVAIVGETV YDDEQTMFVC NTLQPGCNQA CYDRAFPISH IRYWVFQIIM VCTPSLCFIT YSVHQSAKQ RERRADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGFD I LVGQIDDA ...String:
MQHSTMIGRI LLTVVVIFRI LIVAIVGETV YDDEQTMFVC NTLQPGCNQA CYDRAFPISH IRYWVFQIIM VCTPSLCFIT YSVHQSAKQ RERRADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGFD I LVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LKLRRQEGIS RFYIIQVVFR NALEIGFLVG QYFLYGFSVP GL YECNRYP CIKEVECYVS RPTEKTVFLV FMFAVSGICV VLNLAELNHL GWRKIKLAVR GAQAKRKSIY EIRNKDLPRV SVP NFGRTQ SSDSAYVSRD YKDDDDK

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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: 48 / 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: 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

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39444

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