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- PDB-7xki: Human Cx36/GJD2 (N-terminal deletion BRIL-fused mutant) gap junct... -

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Basic information

Entry
Database: PDB / ID: 7xki
TitleHuman Cx36/GJD2 (N-terminal deletion BRIL-fused mutant) gap junction channel in soybean lipids (D6 symmetry)
ComponentsGap junction delta-2 protein,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / connexin 36 / Gap Junction Channel / Cx36 / GJD2 / BRIL
Function / homology
Function and homology information


Electric Transmission Across Gap Junctions / connexin complex / gap junction channel activity / Gap junction assembly / neuronal action potential / visual perception / electron transport chain / cell-cell signaling / chemical synaptic transmission / periplasmic space ...Electric Transmission Across Gap Junctions / connexin complex / gap junction channel activity / Gap junction assembly / neuronal action potential / visual perception / electron transport chain / cell-cell signaling / chemical synaptic transmission / periplasmic space / electron transfer activity / iron ion binding / heme binding / 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 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
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Soluble cytochrome b562 / Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCho, H.J. / Lee, S.N. / Jeong, H. / Ryu, B. / Lee, H.J. / Woo, J.S. / Lee, H.H.
Funding support Korea, Republic Of, 2items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Mar 22, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Mar 22, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Mar 22, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 22, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 25, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gap junction delta-2 protein,Soluble cytochrome b562
B: Gap junction delta-2 protein,Soluble cytochrome b562
C: Gap junction delta-2 protein,Soluble cytochrome b562
D: Gap junction delta-2 protein,Soluble cytochrome b562
E: Gap junction delta-2 protein,Soluble cytochrome b562
F: Gap junction delta-2 protein,Soluble cytochrome b562
G: Gap junction delta-2 protein,Soluble cytochrome b562
H: Gap junction delta-2 protein,Soluble cytochrome b562
I: Gap junction delta-2 protein,Soluble cytochrome b562
J: Gap junction delta-2 protein,Soluble cytochrome b562
K: Gap junction delta-2 protein,Soluble cytochrome b562
L: Gap junction delta-2 protein,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)504,00060
Polymers471,45912
Non-polymers32,54148
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Gap junction delta-2 protein,Soluble cytochrome b562 / Connexin-36 / Cx36 / Gap junction alpha-9 protein / Cytochrome b-562


Mass: 39288.258 Da / Num. of mol.: 12 / Mutation: M29W,H124I,R128L
Source method: isolated from a genetically manipulated source
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
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: GJD2, GJA9, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UKL4, UniProt: P0ABE7
#2: Chemical...
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C36H72NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cx36-BRIL-DelN16 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39444 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00216620
ELECTRON MICROSCOPYf_angle_d0.4222452
ELECTRON MICROSCOPYf_dihedral_angle_d6.5592364
ELECTRON MICROSCOPYf_chiral_restr0.0382604
ELECTRON MICROSCOPYf_plane_restr0.0032748

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