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Yorodumi- PDB-8gyo: Inner channel lipids regulated gating mechanism of human pannexins. -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gyo | ||||||
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Title | Inner channel lipids regulated gating mechanism of human pannexins. | ||||||
Components | Pannexin-1 | ||||||
Keywords | MEMBRANE PROTEIN / Pannexin / ATP / Inner channel lipids / Cell-cell communication | ||||||
Function / homology | Function and homology information ATP transmembrane transporter activity / ATP transport / Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion channel activity / monoatomic anion transmembrane transport / gap junction ...ATP transmembrane transporter activity / ATP transport / Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / wide pore channel activity / bleb / monoatomic anion channel activity / monoatomic anion transmembrane transport / gap junction / gap junction channel activity / positive regulation of macrophage cytokine production / response to ATP / oogenesis / monoatomic cation transport / The NLRP3 inflammasome / positive regulation of interleukin-1 beta production / response to ischemia / calcium channel activity / calcium ion transport / actin filament binding / cell-cell signaling / scaffold protein binding / protease binding / transmembrane transporter binding / signaling receptor binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Cong, Y. / Jin, X. / Kong, F. / Yan, C. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Inner channel lipids regulated gating mechanism of human pannexins. Authors: Cong, Y. / Jin, X. / Kong, F. / Yan, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gyo.cif.gz | 422.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gyo.ent.gz | 351.1 KB | Display | PDB format |
PDBx/mmJSON format | 8gyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gyo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8gyo_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8gyo_validation.xml.gz | 74.2 KB | Display | |
Data in CIF | 8gyo_validation.cif.gz | 105.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/8gyo ftp://data.pdbj.org/pub/pdb/validation_reports/gy/8gyo | HTTPS FTP |
-Related structure data
Related structure data | 34374MC 8gypC 8gyqC 8gytC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 48093.863 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PANX1, MRS1, UNQ2529/PRO6028 / Production host: Homo sapiens (human) / References: UniProt: Q96RD7 #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Chemical | Has ligand of interest | 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: Pannexin-1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.350 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Conc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148994 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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