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Yorodumi- PDB-8jv8: Cryo-EM structure of the panda P2X7 receptor in complex with PPNDS -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jv8 | ||||||
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Title | Cryo-EM structure of the panda P2X7 receptor in complex with PPNDS | ||||||
Components | P2X purinoceptor | ||||||
Keywords | TRANSPORT PROTEIN / Channel | ||||||
Function / homology | Function and homology information purinergic nucleotide receptor activity / extracellularly ATP-gated monoatomic cation channel activity / response to ATP / calcium ion transmembrane transport / postsynapse / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Ailuropoda melanoleuca (giant panda) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å | ||||||
Authors | Sheng, D. / Hattori, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Elife / Year: 2024 Title: Structural insights into the orthosteric inhibition of P2X receptors by non-ATP analog antagonists. Authors: Danqi Sheng / Chen-Xi Yue / Fei Jin / Yao Wang / Muneyoshi Ichikawa / Ye Yu / Chang-Run Guo / Motoyuki Hattori / Abstract: P2X receptors are extracellular ATP-gated ion channels that form homo- or heterotrimers and consist of seven subtypes. They are expressed in various tissues, including neuronal and nonneuronal cells, ...P2X receptors are extracellular ATP-gated ion channels that form homo- or heterotrimers and consist of seven subtypes. They are expressed in various tissues, including neuronal and nonneuronal cells, and play critical roles in physiological processes such as neurotransmission, inflammation, pain, and cancer. As a result, P2X receptors have attracted considerable interest as drug targets, and various competitive inhibitors have been developed. However, although several P2X receptor structures from different subtypes have been reported, the limited structural information of P2X receptors in complex with competitive antagonists hampers the understanding of orthosteric inhibition, hindering the further design and optimization of those antagonists for drug discovery. We determined the cryogenic electron microscopy (cryo-EM) structures of the mammalian P2X7 receptor in complex with two classical competitive antagonists of pyridoxal-5'-phosphate derivatives, pyridoxal-5'-phosphate-6-(2'-naphthylazo-6'-nitro-4',8'-disulfonate) (PPNDS) and pyridoxal phosphate-6-azophenyl-2',5'-disulfonic acid (PPADS), and performed structure-based mutational analysis by patch-clamp recording as well as molecular dynamics (MD) simulations. Our structures revealed the orthosteric site for PPADS/PPNDS, and structural comparison with the previously reported apo- and ATP-bound structures showed how PPADS/PPNDS binding inhibits the conformational changes associated with channel activation. In addition, structure-based mutational analysis identified key residues involved in the PPNDS sensitivity of P2X1 and P2X3, which are known to have higher affinity for PPADS/PPNDS than other P2X subtypes. #1: Journal: Elife / Year: 2023 Title: Structural insights into the orthosteric inhibition of P2X receptors by non-ATP-analog antagonists Authors: Sheng, D. / Yue, C. / Jin, F. / Wang, Y. / Ichikawa, M. / Yu, Y. / Guo, C.R. / Hattori, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jv8.cif.gz | 197.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jv8.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/8jv8 ftp://data.pdbj.org/pub/pdb/validation_reports/jv/8jv8 | HTTPS FTP |
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-Related structure data
Related structure data | 36671MC 8jv7C 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: 38716.234 Da / Num. of mol.: 3 / Mutation: V35A, R125A, E174K, N241S, N284S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ailuropoda melanoleuca (giant panda) / Gene: PANDA_000894 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D2GVW0 #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: P2X7 trimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Ailuropoda melanoleuca (giant panda) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: 2000 nm / Nominal defocus min: 1300 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121008 / Symmetry type: POINT | ||||||||||||||||||||||||
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