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Yorodumi- EMDB-34266: CryoEM structure of human Pannexin1 with R217H congenital mutation. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34266 | |||||||||
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Title | CryoEM structure of human Pannexin1 with R217H congenital mutation. | |||||||||
Map data | human Pannexin 1 R217H mutant | |||||||||
Sample |
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Keywords | Pannexin1 / ATP release / large-pore ion channel / MEMBRANE PROTEIN | |||||||||
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: 3.87 Å | |||||||||
Authors | Hussain N / Penmatsa A | |||||||||
Funding support | India, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cryo-EM structures of pannexin 1 and 3 reveal differences among pannexin isoforms. Authors: Nazia Hussain / Ashish Apotikar / Shabareesh Pidathala / Sourajit Mukherjee / Ananth Prasad Burada / Sujit Kumar Sikdar / Kutti R Vinothkumar / Aravind Penmatsa / Abstract: Pannexins are single-membrane large-pore channels that release ions and ATP upon activation. Three isoforms of pannexins 1, 2, and 3, perform diverse cellular roles and differ in their pore lining ...Pannexins are single-membrane large-pore channels that release ions and ATP upon activation. Three isoforms of pannexins 1, 2, and 3, perform diverse cellular roles and differ in their pore lining residues. In this study, we report the cryo-EM structure of pannexin 3 at 3.9 Å and analyze its structural differences with pannexin isoforms 1 and 2. The pannexin 3 vestibule has two distinct chambers and a wider pore radius in comparison to pannexins 1 and 2. We further report two cryo-EM structures of pannexin 1, with pore substitutions W74R/R75D that mimic the pore lining residues of pannexin 2 and a germline mutant of pannexin 1, R217H at resolutions of 3.2 Å and 3.9 Å, respectively. Substitution of cationic residues in the vestibule of pannexin 1 results in reduced ATP interaction propensities to the channel. The germline mutant R217H in transmembrane helix 3 (TM3), leads to a partially constricted pore, reduced ATP interaction and weakened voltage sensitivity. The study compares the three pannexin isoform structures, the effects of substitutions of pore and vestibule-lining residues and allosteric effects of a pathological substitution on channel structure and function thereby enhancing our understanding of this vital group of ATP-release channels. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34266.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-34266-v30.xml emd-34266.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34266_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_34266.png | 68.7 KB | ||
Filedesc metadata | emd-34266.cif.gz | 6.5 KB | ||
Others | emd_34266_half_map_1.map.gz emd_34266_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34266 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34266 | HTTPS FTP |
-Validation report
Summary document | emd_34266_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_34266_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_34266_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_34266_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34266 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34266 | HTTPS FTP |
-Related structure data
Related structure data | 8gtsMC 8gtrC 8gttC M: atomic model generated by this map 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_34266.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | human Pannexin 1 R217H mutant | ||||||||||||||||||||||||||||||||||||
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 B
File | emd_34266_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_34266_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pannexin 1 (R217H)
Entire | Name: Pannexin 1 (R217H) |
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Components |
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-Supramolecule #1: Pannexin 1 (R217H)
Supramolecule | Name: Pannexin 1 (R217H) / 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: 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: 48.074816 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAIAQLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSWRQAAFV DSYCWAAVQ QKNSLQSESG NLPLWLHKFF PYILLLFAIL LYLPPLFWRF AAAPHICSDL KFIMEELDKV YNRAIKAAKS A RDLDMRDG ...String: MAIAQLATEY VFSDFLLKEP TEPKFKGLRL ELAVDKMVTC IAVGLPLLLI SLAFAQEISI GTQISCFSPS SFSWRQAAFV DSYCWAAVQ QKNSLQSESG NLPLWLHKFF PYILLLFAIL LYLPPLFWRF AAAPHICSDL KFIMEELDKV YNRAIKAAKS A RDLDMRDG ACSVPGVTEN LGQSLWEVSE SHFKYPIVEQ YLKTKKNSNN LIIKYISCHL LTLIIILLAC IYLGYYFSLS SL SDEFVCS IKSGILRNDS TVPDQFQCKL IAVGIFQLLS VINLVVYVLL APVVVYTLFV PFRQKTDVLK VYEILPTFDV LHF KSEGYN DLSLYNLFLE ENISEVKSYK CLKVLENIKS SGQGIDPMLL LTNLGMIKMD VVDGKTPMSA EMREEQGNQT AELQ GMNID SETKANNGEK NARQRLLDSS C UniProtKB: Pannexin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 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 / Details: 25 milli amps for 60s | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV Details: sequentially blotted for 2 and 3.5 seconds with a wait of 10 s.. | |||||||||||||||
Details | Sample is homoheptamer purified to homogeneity. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Specialist optics | Phase plate: OTHER / Spherical aberration corrector: None / Chromatic aberration corrector: None / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: Bioquantum with K2 camera |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1776 / Average electron dose: 41.12 e/Å2 |
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: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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: 156 / Target criteria: Correlation coeficient |
Output model | PDB-8gts: |