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- EMDB-18468: Connexin-43 gap junction channel in complex with mefloquine -

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Basic information

Entry
Database: EMDB / ID: EMD-18468
TitleConnexin-43 gap junction channel in complex with mefloquine
Map data
Sample
  • Complex: Connexin-32 gap junction channel in complex with 2-aminoethoxydipheniyl borate
    • Protein or peptide: Gap junction alpha-1 protein
Keywordsconnexin / gap junction channel / complex / mefloquine / MEMBRANE PROTEIN
Function / homology
Function and homology information


gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / positive regulation of striated muscle tissue development / milk ejection reflex / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / columnar/cuboidal epithelial cell maturation ...gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / positive regulation of striated muscle tissue development / milk ejection reflex / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / columnar/cuboidal epithelial cell maturation / glutathione transmembrane transporter activity / neuroblast migration / gap junction hemi-channel activity / negative regulation of trophoblast cell migration / microtubule-based transport / regulation of bone remodeling / monoatomic ion transmembrane transporter activity / SARS-CoV-2 targets PDZ proteins in cell-cell junction / regulation of ventricular cardiac muscle cell membrane depolarization / gap junction channel activity involved in cell communication by electrical coupling / contractile muscle fiber / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / gap junction assembly / atrial cardiac muscle cell action potential / cellular response to pH / Regulation of gap junction activity / cardiac conduction system development / skeletal muscle tissue regeneration / regulation of atrial cardiac muscle cell membrane depolarization / connexin complex / Golgi-associated vesicle membrane / Formation of annular gap junctions / fascia adherens / Gap junction degradation / export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / cell-cell contact zone / gap junction / bone remodeling / Gap junction assembly / gap junction channel activity / adult heart development / regulation of bone mineralization / glutamate secretion / regulation of ventricular cardiac muscle cell membrane repolarization / tight junction / blood vessel morphogenesis / lens development in camera-type eye / xenobiotic transport / intermediate filament / embryonic digit morphogenesis / maintenance of blood-brain barrier / positive regulation of stem cell proliferation / RHOJ GTPase cycle / heart looping / efflux transmembrane transporter activity / beta-tubulin binding / RHOQ GTPase cycle / establishment of mitotic spindle orientation / intercalated disc / lateral plasma membrane / alpha-tubulin binding / T cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / bone development / tubulin binding / protein tyrosine kinase binding / neuron migration / negative regulation of cell growth / beta-catenin binding / osteoblast differentiation / male gonad development / monoatomic ion transmembrane transport / cellular response to amyloid-beta / protein localization / positive regulation of cold-induced thermogenesis / cell junction / cell-cell signaling / heart development / spermatogenesis / scaffold protein binding / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / apical plasma membrane / membrane raft / Golgi membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / signaling receptor binding / focal adhesion / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily ...Gap junction alpha-1 protein (Cx43) / Gap junction alpha-1 protein (Cx43), C-terminal / Gap junction alpha-1 protein (Cx43), alpha helix domain superfamily / Gap junction alpha-1 protein (Cx43) / Connexin, C-terminal / 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 alpha-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsLavriha P / Korkhov VM / Han Y
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation184951 Switzerland
CitationJournal: To Be Published
Title: Two distinct mechanisms of connexin channel inhibition by mefloquine and 2-aminoethoxydiphenyl borate
Authors: Lavriha P / Han Y / Ding X / Qi C / Vaithia A / Korkhov VM
History
DepositionSep 16, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18468.png

Downloads & links

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Map

FileDownload / File: emd_18468.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 249.911 Å		0.65 Å/pix.
x 384 pix.
= 249.911 Å		0.65 Å/pix.
x 384 pix.
= 249.911 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65081 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0037450218 - 0.014895899
Average (Standard dev.)0.00031888348 (±0.0012410264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 249.91118 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18468_msk_1.map
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AxesZYX

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Half map: half1

Fileemd_18468_half_map_1.map
Annotationhalf1
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Half map: #1

Fileemd_18468_half_map_2.map
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Sample components

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Entire : Connexin-32 gap junction channel in complex with 2-aminoethoxydip...

EntireName: Connexin-32 gap junction channel in complex with 2-aminoethoxydipheniyl borate
Components
  • Complex: Connexin-32 gap junction channel in complex with 2-aminoethoxydipheniyl borate
    • Protein or peptide: Gap junction alpha-1 protein

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Supramolecule #1: Connexin-32 gap junction channel in complex with 2-aminoethoxydip...

SupramoleculeName: Connexin-32 gap junction channel in complex with 2-aminoethoxydipheniyl borate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gap junction alpha-1 protein

MacromoleculeName: Gap junction alpha-1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.061336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPT LLYLAHVFYV MRKEEKLNKK EEELKVAQTD GVNVDMHLKQ IEIKKFKYGI EEHGKVKMRG GLLRTYIISI L FKSIFEVA ...String:
MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPT LLYLAHVFYV MRKEEKLNKK EEELKVAQTD GVNVDMHLKQ IEIKKFKYGI EEHGKVKMRG GLLRTYIISI L FKSIFEVA FLLIQWYIYG FSLSAVYTCK RDPCPHQVDC FLSRPTEKTI FIIFMLVVSL VSLALNIIEL FYVFFKGVKD RV KGKSDPY HATSGALSPA KDCGSQKYAY FNGCSSPTAP LSPMSPPGYK LVTGDRNNSS CRNYNKQASE QNWANYSAEQ NRM GQAGST ISNSHAQPFD FPDDNQNSKK LAAGHELQPL AIVDQRPSSR ASSRASSRPR PDDLEI

UniProtKB: Gap junction alpha-1 protein

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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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMTris-HCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

15010

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 28940
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)

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