+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28902 | |||||||||
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Title | Cryo-EM structure of human pannexin 2 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Electric Transmission Across Gap Junctions / wide pore channel activity / positive regulation of interleukin-1 production / monoatomic cation transport / monoatomic ion transmembrane transport / response to ischemia / electron transport chain / cell-cell signaling / periplasmic space / electron transfer activity ...Electric Transmission Across Gap Junctions / wide pore channel activity / positive regulation of interleukin-1 production / monoatomic cation transport / monoatomic ion transmembrane transport / response to ischemia / electron transport chain / cell-cell signaling / periplasmic space / electron transfer activity / iron ion binding / Golgi membrane / endoplasmic reticulum membrane / heme binding / structural molecule activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.92 Å | |||||||||
Authors | He Z / Yuan P | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural and functional analysis of human pannexin 2 channel. Authors: Zhihui He / Yonghui Zhao / Michael J Rau / James A J Fitzpatrick / Rajan Sah / Hongzhen Hu / Peng Yuan / Abstract: The pannexin 2 channel (PANX2) participates in multiple physiological processes including skin homeostasis, neuronal development, and ischemia-induced brain injury. However, the molecular basis of ...The pannexin 2 channel (PANX2) participates in multiple physiological processes including skin homeostasis, neuronal development, and ischemia-induced brain injury. However, the molecular basis of PANX2 channel function remains largely unknown. Here, we present a cryo-electron microscopy structure of human PANX2, which reveals pore properties contrasting with those of the intensely studied paralog PANX1. The extracellular selectivity filter, defined by a ring of basic residues, more closely resembles that of the distantly related volume-regulated anion channel (VRAC) LRRC8A, rather than PANX1. Furthermore, we show that PANX2 displays a similar anion permeability sequence as VRAC, and that PANX2 channel activity is inhibited by a commonly used VRAC inhibitor, DCPIB. Thus, the shared channel properties between PANX2 and VRAC may complicate dissection of their cellular functions through pharmacological manipulation. Collectively, our structural and functional analysis provides a framework for development of PANX2-specific reagents that are needed for better understanding of channel physiology and pathophysiology. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28902.map.gz | 78.8 MB | EMDB map data format | |
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Header (meta data) | emd-28902-v30.xml emd-28902.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_28902.png | 156.5 KB | ||
Others | emd_28902_half_map_1.map.gz emd_28902_half_map_2.map.gz | 77.5 MB 77.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28902 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28902 | HTTPS FTP |
-Validation report
Summary document | emd_28902_validation.pdf.gz | 838.1 KB | Display | EMDB validaton report |
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Full document | emd_28902_full_validation.pdf.gz | 837.7 KB | Display | |
Data in XML | emd_28902_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_28902_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28902 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28902 | HTTPS FTP |
-Related structure data
Related structure data | 8f7cMC 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_28902.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.9 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28902_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28902_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human pannexin 2
Entire | Name: human pannexin 2 |
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Components |
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-Supramolecule #1: human pannexin 2
Supramolecule | Name: human pannexin 2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 380 KDa |
-Macromolecule #1: Pannexin-2, Soluble cytochrome b562 fusion
Macromolecule | Name: Pannexin-2, Soluble cytochrome b562 fusion / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 55.033406 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MHHLLEQSAD MATALLAGEK LRELILPGAQ DDKAGALAAL LLQLKLELPF DRVVTIGTVL VPILLVTLVF TKNFAEEPIY CYTPHNFTR DQALYARGYC WTELRDALPG VDASLWPSLF EHKFLPYALL AFAAIMYVPA LGWEFLASTR LTSELNFLLQ E IDNCYHRA ...String: MHHLLEQSAD MATALLAGEK LRELILPGAQ DDKAGALAAL LLQLKLELPF DRVVTIGTVL VPILLVTLVF TKNFAEEPIY CYTPHNFTR DQALYARGYC WTELRDALPG VDASLWPSLF EHKFLPYALL AFAAIMYVPA LGWEFLASTR LTSELNFLLQ E IDNCYHRA AEGRAPKIEK QIQSKGPGIT EREKREIIEN AEKEKSPEQN LFEKYLERRG RSNFLAKLYL ARHVLILLLS AV PISYLCT YYATQKQNEF TCALGASPDG AAGAGPAVRV SCKLPSVQLQ RIIAGVDIVL LCVMNLIILV NLIHLFIFRK SNF IFDKLH KVGIKTRRQW RRSQFCDINI LAMFCNENRD HIKSLNRLDF ITNESDADLE DNWETLNDNL KVIEKADNAA QVKD ALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLSN SLEV LFQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.5 mg/mL |
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Buffer | pH: 8 Details: 20mM Tris-HCL, 150mM NaCl, 40uM GDN, 1mM Fluorinated Fos-Choline-8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 78.73 |
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Output model | PDB-8f7c: |