+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34268 | |||||||||
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Title | human Pannexin1 | |||||||||
Map data | human Pannexin1 structure | |||||||||
Sample |
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Keywords | Pannexin1 / ATP release / large-pore ion channel. / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / bleb / wide pore channel activity / gap junction channel activity / gap junction / positive regulation of macrophage cytokine production / oogenesis / response to ATP ...Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / bleb / wide pore channel activity / gap junction channel activity / gap junction / positive regulation of macrophage cytokine production / oogenesis / response to ATP / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Hussain N / Penmatsa A / Vinothkumar KR | |||||||||
Funding support | India, 1 items
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Citation | Journal: To Be Published Title: Structural insights into pore dynamics of human Pannexin isoforms Authors: Hussain N / Apotikar A / Pidathala S / Mukherjee S / Burada AP / Sikdar SK / Vinothkumar KR / Penmatsa A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34268.map.gz | 167.9 MB | EMDB map data format | |
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Header (meta data) | emd-34268-v30.xml emd-34268.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34268_fsc.xml | 13.4 KB | Display | FSC data file |
Images | emd_34268.png | 63.2 KB | ||
Filedesc metadata | emd-34268.cif.gz | 5.7 KB | ||
Others | emd_34268_half_map_1.map.gz emd_34268_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34268 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34268 | HTTPS FTP |
-Related structure data
Related structure data | 8gtrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34268.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | human Pannexin1 structure | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A
File | emd_34268_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_34268_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pannexin 1
Entire | Name: Pannexin 1PANX1 |
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Components |
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-Supramolecule #1: Pannexin 1
Supramolecule | Name: Pannexin 1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all Details: human isoform 1 of Pannexin. Expressed in plasma membranes involved in ATP release |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 48 kDa/nm |
-Macromolecule #1: human Pannexin1
Macromolecule | Name: human Pannexin1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAIAQLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSWRQAAFV DSYCWAAVQQ KNSLQSESGN LPLWLHKFFP YILLLFAILL YLPPLFWRFA AAPHICSDLK FIMEELDKVY NRAIKAAKSA RDLDMRDGAC ...String: MAIAQLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSWRQAAFV DSYCWAAVQQ KNSLQSESGN LPLWLHKFFP YILLLFAILL YLPPLFWRFA AAPHICSDLK FIMEELDKVY NRAIKAAKSA RDLDMRDGAC SVPGVTENLG QSLWEVSESH FKYPIVEQYL KTKKNSNNLI IKYISCRLLT LIIILLACIY LGYYFSLSSL SDEFVCSIKS GILRNDSTVP DQFQCKLIAV GIFQLLSVIN LVVYVLLAPV VVYTLFVPFR QKTDVLKVYE ILPTFDVLHF KSEGYNDLSL YNLFLEENIS EVKSYKCLKV LENIKSSGQG IDPMLLLTNL GMIKMDVVDG KTPMSAEMRE EQGNQTAELQ GMNIDSETKA NNGEKNARQR LLDSSC UniProtKB: Pannexin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
Details: Fresh solution containing detergent was prepared for every prep. | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: 3.5 s single blot. | |||||||||||||||
Details | Sample is homoheptamer purified to homogeneity. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 75000 |
Specialist optics | Phase plate: OTHER / Spherical aberration corrector: None / Chromatic aberration corrector: None / Details: Falcon III |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 100.0 K / Max: 100.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1205 / Average electron dose: 29.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 179.6 / Target criteria: Correlation coeficient |