+Open data
-Basic information
Entry | Database: PDB / ID: 7jn1 | |||||||||
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Title | Sheep Connexin-46 at 2.5 angstroms resolution, Lipid Class 3 | |||||||||
Components | Gap junction alpha-3 protein | |||||||||
Keywords | MEMBRANE PROTEIN / Connexin / Gap Junction / Lipid / Nanodisc | |||||||||
Function / homology | Function and homology information gap junction hemi-channel activity / gap junction-mediated intercellular transport / cell communication / connexin complex / visual perception / plasma membrane Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Flores, J.A. / Haddad, B.G. / Dolan, K.D. / Myers, J.B. / Yoshioka, C.C. / Copperman, J. / Zuckerman, D.M. / Reichow, S.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å. Authors: Jonathan A Flores / Bassam G Haddad / Kimberly A Dolan / Janette B Myers / Craig C Yoshioka / Jeremy Copperman / Daniel M Zuckerman / Steve L Reichow / Abstract: Gap junctions establish direct pathways for cells to transfer metabolic and electrical messages. The local lipid environment is known to affect the structure, stability and intercellular channel ...Gap junctions establish direct pathways for cells to transfer metabolic and electrical messages. The local lipid environment is known to affect the structure, stability and intercellular channel activity of gap junctions; however, the molecular basis for these effects remains unknown. Here, we incorporate native connexin-46/50 (Cx46/50) intercellular channels into a dual lipid nanodisc system, mimicking a native cell-to-cell junction. Structural characterization by CryoEM reveals a lipid-induced stabilization to the channel, resulting in a 3D reconstruction at 1.9 Å resolution. Together with all-atom molecular dynamics simulations, it is shown that Cx46/50 in turn imparts long-range stabilization to the dynamic local lipid environment that is specific to the extracellular lipid leaflet. In addition, ~400 water molecules are resolved in the CryoEM map, localized throughout the intercellular permeation pathway and contributing to the channel architecture. These results illustrate how the aqueous-lipid environment is integrated with the architectural stability, structure and function of gap junction communication channels. #1: Journal: BioRxiv / Year: 2020 Title: Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 angstroms Authors: Flores, J.A. / Haddad, B.G. / Dolan, K.A. / Myers, J.B. / Yoshioka, C.C. / Copperman, J. / Zuckerman, D.M. / Reichow, S.L. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jn1.cif.gz | 969 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jn1.ent.gz | 799.1 KB | Display | PDB format |
PDBx/mmJSON format | 7jn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jn1_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 7jn1_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 7jn1_validation.xml.gz | 83.8 KB | Display | |
Data in CIF | 7jn1_validation.cif.gz | 106 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/7jn1 ftp://data.pdbj.org/pub/pdb/validation_reports/jn/7jn1 | HTTPS FTP |
-Related structure data
Related structure data | 22391MC 7jjpC 7jkcC 7jlwC 7jm9C 7jmcC 7jmdC 7jn0C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10480 (Title: Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å Data size: 4.1 TB Data #1: Unaligned multiframe micrographs of sheep lens Connexin-46/50 gap junctions embedded in MSP1E1 lipid nanodiscs [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 44033.027 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: Eye / Plasmid details: Young Sheep / Tissue: Lens / References: UniProt: Q9TU17 #2: Chemical | ChemComp-MC3 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Connexin-46 / Type: COMPLEX / Source: NATURAL |
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Molecular weight | Value: 0.45 MDa / Experimental value: NO |
Source (natural) | Organism: Ovis aries (sheep) / Organ: Eye / Tissue: Lens |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 30 sec. / Electron dose: 52.5 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2088 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6942 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6MHQ Accession code: 6MHQ / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.19 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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