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Yorodumi- EMDB-32768: Cryo-EM structure of the N-terminal deletion mutant of human pann... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32768 | ||||||||||||
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Title | Cryo-EM structure of the N-terminal deletion mutant of human pannexin-1 in a nanodisc | ||||||||||||
Map data | 3D map of the N-terminal deletion mutant of human pannexin-1 | ||||||||||||
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 / 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 | single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||||||||
Authors | Kuzuya M / Hirano H / Hayashida K / Watanabe M / Kobayashi K / Tani K / Fujiyoshi Y / Oshima A | ||||||||||||
Funding support | Japan, 3 items
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Citation | Journal: Sci Signal / Year: 2022 Title: Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids. Authors: Maki Kuzuya / Hidemi Hirano / Kenichi Hayashida / Masakatsu Watanabe / Kazumi Kobayashi / Tohru Terada / Md Iqbal Mahmood / Florence Tama / Kazutoshi Tani / Yoshinori Fujiyoshi / Atsunori Oshima / Abstract: Pannexin (PANX) family proteins form large-pore channels that mediate purinergic signaling. We analyzed the cryo-EM structures of human PANX1 in lipid nanodiscs to elucidate the gating mechanism and ...Pannexin (PANX) family proteins form large-pore channels that mediate purinergic signaling. We analyzed the cryo-EM structures of human PANX1 in lipid nanodiscs to elucidate the gating mechanism and its regulation by the amino terminus in phospholipids. The wild-type channel has an amino-terminal funnel in the pore, but in the presence of the inhibitor probenecid, a cytoplasmically oriented amino terminus and phospholipids obstruct the pore. Functional analysis using whole-cell patch-clamp and oocyte voltage clamp showed that PANX1 lacking the amino terminus did not open and had a dominant negative effect on channel activity, thus confirming that the amino-terminal domain played an essential role in channel opening. These observations suggest that dynamic conformational changes in the amino terminus of human PANX1 are associated with lipid movement in and out of the pore. Moreover, the data provide insight into the gating mechanism of PANX1 and, more broadly, other large-pore channels. | ||||||||||||
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_32768.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-32768-v30.xml emd-32768.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32768_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_32768.png | 223.6 KB | ||
Masks | emd_32768_msk_1.map | 15.6 MB | Mask map | |
Others | emd_32768_half_map_1.map.gz emd_32768_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32768 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32768 | HTTPS FTP |
-Validation report
Summary document | emd_32768_validation.pdf.gz | 702.7 KB | Display | EMDB validaton report |
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Full document | emd_32768_full_validation.pdf.gz | 702.3 KB | Display | |
Data in XML | emd_32768_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | emd_32768_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32768 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32768 | HTTPS FTP |
-Related structure data
Related structure data | 7wsvMC 7f8jC 7f8nC 7f8oC 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_32768.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D map of the N-terminal deletion mutant of human pannexin-1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.232 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_32768_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32768_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32768_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Heptamar of N-terminal deleted human pannexin-1 in a nanodisc
Entire | Name: Heptamar of N-terminal deleted human pannexin-1 in a nanodisc |
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Components |
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-Supramolecule #1: Heptamar of N-terminal deleted human pannexin-1 in a nanodisc
Supramolecule | Name: Heptamar of N-terminal deleted human pannexin-1 in a nanodisc type: complex / Chimera: Yes / 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: 45.955438 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTEPKFKGLR LELAVDKMVT CIAVGLPLLL ISLAFAQEIS IGTQISCFSP SSFSWRQAAF VDSYCWAAVQ QKNSLQSESG NLPLWLHKF FPYILLLFAI LLYLPPLFWR FAAAPHICSD LKFIMEELDK VYNRAIKAAK SARDLDMRDG ACSVPGVTEN L GQSLWEVS ...String: MTEPKFKGLR LELAVDKMVT CIAVGLPLLL ISLAFAQEIS IGTQISCFSP SSFSWRQAAF VDSYCWAAVQ QKNSLQSESG NLPLWLHKF FPYILLLFAI LLYLPPLFWR FAAAPHICSD LKFIMEELDK VYNRAIKAAK SARDLDMRDG ACSVPGVTEN L GQSLWEVS ESHFKYPIVE QYLKTKKNSN NLIIKYISCR LLTLIIILLA CIYLGYYFSL SSLSDEFVCS IKSGILRNDS TV PDQFQCK LIAVGIFQLL SVINLVVYVL LAPVVVYTLF VPFRQKTDVL KVYEILPTFD VLHFKSEGYN DLSLYNLFLE ENI SEVKSY KCLKVLENIK SSGQGIDPML LLTNLGMIKM DVVDGKTPMS AEMREEQGNQ TAELQGMNID SETKANNGEK NARQ RLLDS SC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.1 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: pH 7.5 was used. | |||||||||
Grid | Model: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA KF80 Details: Blot for 10 seconds at room temperature followed by plunge freezing. Humidity and temperature are not controlled.. |
-Electron microscopy
Microscope | JEOL 3000SFF |
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Temperature | Min: 80.0 K / Max: 100.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 3587 / Average exposure time: 8.0 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.4000000000000001 µm / Calibrated magnification: 40600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder model: JEOL / Cooling holder cryogen: HELIUM |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 344.6 |
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Output model | PDB-7wsv: |