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- PDB-8r7r: human connexin36 gap junction channel in complex with quinidine -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8r7r
Titlehuman connexin36 gap junction channel in complex with quinidine
ComponentsGap junction delta-2 protein
KeywordsMEMBRANE PROTEIN / connexin in complex with inhibitor
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 / 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
Quinidine / Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsDing, X.Y. / Blum, T.B. / Korkhov, V.M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Cell Discov / Year: 2024
Title: Structural basis of connexin-36 gap junction channel inhibition.
Authors: Xinyue Ding / Simone Aureli / Anand Vaithia / Pia Lavriha / Dina Schuster / Basavraj Khanppnavar / Xiaodan Li / Thorsten B Blum / Paola Picotti / Francesco L Gervasio / Volodymyr M Korkhov /
History
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2May 14, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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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
B: Gap junction delta-2 protein
C: Gap junction delta-2 protein
D: Gap junction delta-2 protein
E: Gap junction delta-2 protein
F: Gap junction delta-2 protein
G: Gap junction delta-2 protein
H: Gap junction delta-2 protein
I: Gap junction delta-2 protein
J: Gap junction delta-2 protein
K: Gap junction delta-2 protein
L: Gap junction delta-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,83824
Polymers444,94512
Non-polymers3,89312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Gap junction delta-2 protein


Mass: 37078.766 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GJD2 / Production host: Homo sapiens (human) / References: UniProt: Q9UKL4
#2: Chemical
ChemComp-QDN / Quinidine / (9S)-6'-methoxycinchonan-9-ol


Mass: 324.417 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H24N2O2 / Feature type: SUBJECT OF INVESTIGATION
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: human connexin36 gap junction channel in complex with quinidine
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: 2000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39915 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317460
ELECTRON MICROSCOPYf_angle_d0.49923748
ELECTRON MICROSCOPYf_dihedral_angle_d5.9942568
ELECTRON MICROSCOPYf_chiral_restr0.042772
ELECTRON MICROSCOPYf_plane_restr0.0032868

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