+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34376 | |||||||||
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Title | Cryo-EM structure of human Pannexin-2 in pre-open state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Pannexin / ATP / Inner channel lipids / Cell-cell communication / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Electric Transmission Across Gap Junctions / wide pore channel activity / positive regulation of interleukin-1 production / monoatomic cation transport / response to ischemia / cell-cell signaling / monoatomic ion transmembrane transport / Golgi membrane / endoplasmic reticulum membrane / structural molecule activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Cong Y / Jin X / Kong F / Yan C | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Inner channel lipids regulated gating mechanism of human pannexins. Authors: Cong Y / Jin X / Kong F / Yan C | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34376.map.gz | 59.8 MB | EMDB map data format | |
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Header (meta data) | emd-34376-v30.xml emd-34376.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_34376.png | 133.9 KB | ||
Masks | emd_34376_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-34376.cif.gz | 5.6 KB | ||
Others | emd_34376_half_map_1.map.gz emd_34376_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34376 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34376 | HTTPS FTP |
-Validation report
Summary document | emd_34376_validation.pdf.gz | 888.7 KB | Display | EMDB validaton report |
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Full document | emd_34376_full_validation.pdf.gz | 888.3 KB | Display | |
Data in XML | emd_34376_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_34376_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34376 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34376 | HTTPS FTP |
-Related structure data
Related structure data | 8gyqMC 8gyoC 8gypC 8gytC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34376.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-Mask #1
File | emd_34376_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34376_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34376_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pannexin-2
Entire | Name: Pannexin-2 |
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Components |
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-Supramolecule #1: Pannexin-2
Supramolecule | Name: Pannexin-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Pannexin-2
Macromolecule | Name: Pannexin-2 / 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: 74.54193 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 ITNESDLMYD NVVRQLLAAL AQSNHDATPT VRDS GVQTV DPSANPAEPD GAAEPPVVKR PRKKMKWIPT SNPLPQPFKE PLAIMRVENS KAEKPKPARR KTATDTLIAP LLDRS AHHY KGGGGDPGPG PAPAPAPPPA PDKKHARHFS LDVHPYILGT KKAKAEAVPA ALPASRSQEG GFLSQAEDCG LGLAPA PIK DAPLPEKEIP YPTEPARAGL PSGGPFHVRS PPAAPAVAPL TPASLGKAEP LTILSRNATH PLLHINTLYE AREEEDG GP RLPQDVGDLI AIPAPQQILI ATFDEPRTVV STVEF UniProtKB: Pannexin-2 |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 7 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.8 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 K3 (6k x 4k) / Average electron dose: 50.0 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: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 131444 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |