+Open data
-Basic information
Entry | Database: PDB / ID: 6vd7 | ||||||
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Title | Cryo-EM structure of Xenopus tropicalis pannexin 1 channel | ||||||
Components | Pannexin | ||||||
Keywords | TRANSPORT PROTEIN / channel / ATP release / heptamer | ||||||
Function / homology | Function and homology information positive regulation of interleukin-1 production / gap junction / channel activity / monoatomic cation transport / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Xenopus tropicalis (tropical clawed frog) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å | ||||||
Authors | Syrjanen, J.L. / Michalski, M. / Furukawa, H. / Kawate, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 Title: The Cryo-EM structure of pannexin 1 reveals unique motifs for ion selection and inhibition. Authors: Kevin Michalski / Johanna L Syrjanen / Erik Henze / Julia Kumpf / Hiro Furukawa / Toshimitsu Kawate / Abstract: Pannexins are large-pore forming channels responsible for ATP release under a variety of physiological and pathological conditions. Although predicted to share similar membrane topology with other ...Pannexins are large-pore forming channels responsible for ATP release under a variety of physiological and pathological conditions. Although predicted to share similar membrane topology with other large-pore forming proteins such as connexins, innexins, and LRRC8, pannexins have minimal sequence similarity to these protein families. Here, we present the cryo-EM structure of a frog pannexin 1 (Panx1) channel at 3.0 Å. We find that Panx1 protomers harbor four transmembrane helices similar in arrangement to other large-pore forming proteins but assemble as a heptameric channel with a unique constriction formed by Trp74 in the first extracellular loop. Mutating Trp74 or the nearby Arg75 disrupt ion selectivity, whereas altering residues in the hydrophobic groove formed by the two extracellular loops abrogates channel inhibition by carbenoxolone. Our structural and functional study establishes the extracellular loops as important structural motifs for ion selectivity and channel inhibition in Panx1. | ||||||
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 | 6vd7.cif.gz | 359.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vd7.ent.gz | 302.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vd7_validation.pdf.gz | 969 KB | Display | wwPDB validaton report |
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Full document | 6vd7_full_validation.pdf.gz | 984.3 KB | Display | |
Data in XML | 6vd7_validation.xml.gz | 56 KB | Display | |
Data in CIF | 6vd7_validation.cif.gz | 75.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/6vd7 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vd7 | HTTPS FTP |
-Related structure data
Related structure data | 21150MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 39424.148 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: panx1, igdcc4, LOC100170473, nell1, PANX / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B3DLA5 |
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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: Heptameric pannexin1 complex assembly / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Xenopus tropicalis (tropical clawed frog) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified / Grid material: COPPER |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 288.15 K |
-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 |
Image recording | Electron dose: 57.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90185 / Symmetry type: POINT | ||||||||||||||||||||||||
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