+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30880 | |||||||||
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Title | Human Pannexin1 model | |||||||||
Map data | ||||||||||
Sample |
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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 / monoatomic anion channel activity / bleb / wide pore channel activity / monoatomic anion transmembrane transport / gap junction channel activity ...ATP transmembrane transporter activity / ATP transport / Electric Transmission Across Gap Junctions / leak channel activity / positive regulation of interleukin-1 alpha production / monoatomic anion channel activity / bleb / wide pore channel activity / monoatomic anion transmembrane transport / 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: 3.15 Å | |||||||||
Authors | Zhang SS / Yang MJ | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2021 Title: Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis. Authors: Sensen Zhang / Baolei Yuan / Jordy Homing Lam / Jun Zhou / Xuan Zhou / Gerardo Ramos-Mandujano / Xueyuan Tian / Yang Liu / Renmin Han / Yu Li / Xin Gao / Mo Li / Maojun Yang / Abstract: Pannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In ...Pannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30880.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-30880-v30.xml emd-30880.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_30880.png | 28 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30880 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30880 | HTTPS FTP |
-Related structure data
Related structure data | 7dwbMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30880.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : plasma membaren channel
Entire | Name: plasma membaren channel |
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Components |
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-Supramolecule #1: plasma membaren channel
Supramolecule | Name: plasma membaren channel / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Pannexin-1
Macromolecule | Name: Pannexin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 49.014824 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AIAHLATEYV FSDFLLKEPT EPKFKGLRLE LAVDKMVTCI AVGLPLLLIS LAFAQEISIG TQISCFSPSS FSWRQAAFVD SYCWAAVQQ KNSLQSESGN LPLWLHKFFP YILLLFAILL YLPPLFWRFA AAPHICSDLK FIMEELDKVY NRAIKAAKSA R DLDMRDGA ...String: AIAHLATEYV FSDFLLKEPT EPKFKGLRLE LAVDKMVTCI AVGLPLLLIS LAFAQEISIG TQISCFSPSS FSWRQAAFVD SYCWAAVQQ KNSLQSESGN LPLWLHKFFP YILLLFAILL YLPPLFWRFA AAPHICSDLK FIMEELDKVY NRAIKAAKSA R DLDMRDGA CSVWSHPQFE KPGVTENLGQ SLWEVSESHF KYPIVEQYLK TKKNSNNLII KYISCRLLTL IIILLACIYL GY YFSLSSL SDEFVCSIKS GILRNDSTVP DQFQCKLIAV GIFQLLSVIN LVVYVLLAPV VVYTLFVPFR QKTDVLKVYE ILP TFDVLH FKSEGYNDLS LYNLFLEENI SEVKSYKCLK VLENIKSSGQ GIDPMLLLTN LGMIKMDVVD GKTPMSAEMR EEQG NQTAE LQGMNIDSET KANNGEKNAR QRLLDSSC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: OTHER |
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Final angle assignment | Type: OTHER |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110000 |