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- EMDB-18540: human connexin-36 gap junction channel in complex with mefloquine -

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Basic information

Entry
Database: EMDB / ID: EMD-18540
Titlehuman connexin-36 gap junction channel in complex with mefloquine
Map data
Sample
  • Complex: human connexin-36 gap junction channel in complex with mefloquine
    • Protein or peptide: Gap junction delta-2 protein
  • Ligand: (11R,12S)- Mefloquine
  • Ligand: water
KeywordsMEMBRANE PROTEIN
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
Gap junction delta-2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.13 Å
AuthorsDing XY / Blum TB / Korkhov VM
Funding support Switzerland, 1 items
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
DepositionSep 29, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18540.png

Downloads & links

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Map

FileDownload / File: emd_18540.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 264. Å		0.66 Å/pix.
x 400 pix.
= 264. Å		0.66 Å/pix.
x 400 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.031
Minimum - Maximum-0.07716879 - 0.14302854
Average (Standard dev.)0.000025597905 (±0.0049137957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18540_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18540_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18540_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : human connexin-36 gap junction channel in complex with mefloquine

EntireName: human connexin-36 gap junction channel in complex with mefloquine
Components
  • Complex: human connexin-36 gap junction channel in complex with mefloquine
    • Protein or peptide: Gap junction delta-2 protein
  • Ligand: (11R,12S)- Mefloquine
  • Ligand: water

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Supramolecule #1: human connexin-36 gap junction channel in complex with mefloquine

SupramoleculeName: human connexin-36 gap junction channel in complex with mefloquine
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: 37.078766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGEWTILERL LEAAVQQHST MIGRILLTVV VIFRILIVAI VGETVYDDEQ TMFVCNTLQP GCNQACYDRA FPISHIRYWV FQIIMVCTP SLCFITYSVH QSAKQRERRY STVFLALDRD PPESIGGPGG TGGGGSGGGK REDKKLQNAI VNGVLQNTEN T SKETEPDC ...String:
MGEWTILERL LEAAVQQHST MIGRILLTVV VIFRILIVAI VGETVYDDEQ TMFVCNTLQP GCNQACYDRA FPISHIRYWV FQIIMVCTP SLCFITYSVH QSAKQRERRY STVFLALDRD PPESIGGPGG TGGGGSGGGK REDKKLQNAI VNGVLQNTEN T SKETEPDC LEVKELTPHP SGLRTASKSK LRRQEGISRF YIIQVVFRNA LEIGFLVGQY FLYGFSVPGL YECNRYPCIK EV ECYVSRP TEKTVFLVFM FAVSGICVVL NLAELNHLGW RKIKLAVRGA QAKRKSIYEI RNKDLPRVSV PNFGRTQSSD SAY VAAALE VLFQ

UniProtKB: Gap junction delta-2 protein

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Macromolecule #2: (11R,12S)- Mefloquine

MacromoleculeName: (11R,12S)- Mefloquine / type: ligand / ID: 2 / Number of copies: 12 / Formula: YMZ
Molecular weightTheoretical: 378.312 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 162 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: The SWISS-MODEL homology model based on connexin-50 GJC (PDB ID 7JJP) of Cx36 was used as a guide for the apo-Cx36 structure. The apo-Cx36 was then used as a template for building the Cx36-mfq.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102585
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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