+Open data
-Basic information
Entry | Database: PDB / ID: 7xlb | ||||||||||||
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Title | Cryo-EM structure of human pannexin 2 | ||||||||||||
Components | Pannexin-2 | ||||||||||||
Keywords | MEMBRANE PROTEIN / ATP channel / Calcium channel / heptamer | ||||||||||||
Function / homology | Function and homology information Electric Transmission Across Gap Junctions / wide pore channel activity / positive regulation of interleukin-1 production / gap junction / monoatomic cation transport / monoatomic ion transmembrane transport / response to ischemia / cell-cell signaling / structural molecule activity / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å | ||||||||||||
Authors | Hang, Z. / Huawei, Z. / Daping, W. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of human heptameric pannexin 2 channel Authors: Zhang, H. / Wang, S. / Zhang, Z. / Hou, M. / Du, C. / Zhao, Z. / Vogel, H. / Li, Z. / Yan, K. / Zhang, X. / Lu, J. / Liang, Y. / Yuan, S. / Wang, D. / Zhang, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xlb.cif.gz | 561.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xlb.ent.gz | 377.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/7xlb ftp://data.pdbj.org/pub/pdb/validation_reports/xl/7xlb | HTTPS FTP |
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-Related structure data
Related structure data | 33276MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 46301.543 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PANX2 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q96RD6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Heptamer of human pannexin 2 channel / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.323 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: 293F | ||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
Image scans | Movie frames/image: 32 |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108265 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.88 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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