+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20964 | |||||||||
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Title | Cryo-EM structure of Xenopus tropicalis pannexin 1 | |||||||||
Map data | Cryo-EM structure of Xenopus tropicalis pannexin 1 | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of interleukin-1 production / gap junction / channel activity / monoatomic cation transport / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Xenopus tropicalis (tropical clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | |||||||||
Authors | Deng Z / He Z / Yuan P | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Cryo-EM structures of the ATP release channel pannexin 1. Authors: Zengqin Deng / Zhihui He / Grigory Maksaev / Ryan M Bitter / Michael Rau / James A J Fitzpatrick / Peng Yuan / Abstract: The plasma membrane adenosine triphosphate (ATP) release channel pannexin 1 (PANX1) has been implicated in many physiological and pathophysiological processes associated with purinergic signaling, ...The plasma membrane adenosine triphosphate (ATP) release channel pannexin 1 (PANX1) has been implicated in many physiological and pathophysiological processes associated with purinergic signaling, including cancer progression, apoptotic cell clearance, inflammation, blood pressure regulation, oocyte development, epilepsy and neuropathic pain. Here we present near-atomic-resolution structures of human and frog PANX1 determined by cryo-electron microscopy that revealed a heptameric channel architecture. Compatible with ATP permeation, the transmembrane pore and cytoplasmic vestibule were exceptionally wide. An extracellular tryptophan ring located at the outer pore created a constriction site, potentially functioning as a molecular sieve that restricts the size of permeable substrates. The amino and carboxyl termini, not resolved in the density map, appeared to be structurally dynamic and might contribute to narrowing of the pore during channel gating. In combination with functional characterization, this work elucidates the previously unknown architecture of pannexin channels and establishes a foundation for understanding their unique channel properties. | |||||||||
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_20964.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-20964-v30.xml emd-20964.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_20964.png | 88.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20964 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20964 | HTTPS FTP |
-Validation report
Summary document | emd_20964_validation.pdf.gz | 464.7 KB | Display | EMDB validaton report |
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Full document | emd_20964_full_validation.pdf.gz | 464.2 KB | Display | |
Data in XML | emd_20964_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_20964_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20964 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20964 | HTTPS FTP |
-Related structure data
Related structure data | 6uzyMC 6v6dC 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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-Map
File | Download / File: emd_20964.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Xenopus tropicalis pannexin 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 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 : xenopus pannexin 1
Entire | Name: xenopus pannexin 1 |
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Components |
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-Supramolecule #1: xenopus pannexin 1
Supramolecule | Name: xenopus pannexin 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Xenopus tropicalis (tropical clawed frog) |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
-Macromolecule #1: Pannexin
Macromolecule | Name: Pannexin / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus tropicalis (tropical clawed frog) |
Molecular weight | Theoretical: 49.735441 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MAIAHIATEY VFSDFLLKDP PESKYKGLRL ELAVDKLVSC IAVGLPLLLI SLAFAQEITL GSQISCFAPT SFSWRQAAYV DSFCWAAVQ QKHLSQSDSG NVPLWLHKFF PYILLLVAVL LYLPNLFWRF TAAPHLSSDL KFVMEELDKC YNRDIKDIKA A NNLNSSDK ...String: MAIAHIATEY VFSDFLLKDP PESKYKGLRL ELAVDKLVSC IAVGLPLLLI SLAFAQEITL GSQISCFAPT SFSWRQAAYV DSFCWAAVQ QKHLSQSDSG NVPLWLHKFF PYILLLVAVL LYLPNLFWRF TAAPHLSSDL KFVMEELDKC YNRDIKDIKA A NNLNSSDK RDGLNSPVVS ENLQQSLWEI PLSHYKYPIV EQYLKTKNNS YGLIIKYLIC RVVTLIIVFT ACIYLGYYIS LF SLTDEFT CNIRTGILRN DTALPPLVQC KLIAVGVFRL LSYINLIIYV LIMPFIIYAM LVPFRKTANV LKVYEVLPTF SVQ QAPSKT YDDHSLFLLF LEENVSELKS YKFLKVLENI KNTGENFDTI QYLTSLGTVK TDTVDGKLAF KCTSEVPNNT EQNE VELTV QPSSDNAKTE EKKVRQRLLD SSCSNSLEVL FQ |
-Macromolecule #2: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...
Macromolecule | Name: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate type: ligand / ID: 2 / Number of copies: 7 / Formula: 6OU |
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Molecular weight | Theoretical: 717.996 Da |
Chemical component information | ChemComp-6OU: |
-Macromolecule #3: HEXADECANE
Macromolecule | Name: HEXADECANE / type: ligand / ID: 3 / Number of copies: 14 / Formula: R16 |
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Molecular weight | Theoretical: 226.441 Da |
Chemical component information | ChemComp-R16: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176371 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |