+Open data
-Basic information
Entry | Database: PDB / ID: 8e6u | ||||||
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Title | Human TRPM2 ion channel in 1 mM F-dADPR | ||||||
Components | Transient receptor potential cation channel subfamily M member 2 | ||||||
Keywords | MEMBRANE PROTEIN / TRPM2 / TRP / ADPR / ADP-ribose / NUDT9H / NUDT9 / calcium / ion channel | ||||||
Function / homology | Function and homology information cellular response to purine-containing compound / mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / zinc ion transmembrane transport / dendritic cell differentiation / response to purine-containing compound / regulation of filopodium assembly / ligand-gated calcium channel activity / cellular response to temperature stimulus / dendritic cell chemotaxis ...cellular response to purine-containing compound / mono-ADP-D-ribose binding / manganese ion transmembrane transporter activity / zinc ion transmembrane transport / dendritic cell differentiation / response to purine-containing compound / regulation of filopodium assembly / ligand-gated calcium channel activity / cellular response to temperature stimulus / dendritic cell chemotaxis / TRP channels / sodium channel activity / calcium ion transmembrane import into cytosol / response to hydroperoxide / temperature homeostasis / calcium ion import across plasma membrane / intracellularly gated calcium channel activity / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cell projection / regulation of actin cytoskeleton organization / calcium ion transmembrane transport / cytoplasmic vesicle membrane / calcium channel activity / cellular response to hydrogen peroxide / calcium ion transport / response to heat / perikaryon / protein homotetramerization / lysosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Wang, L. / Fu, T.M. / Xia, S. / Wu, H. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: A unified mechanism for human TRPM2 activation, desensitization and inhibition Authors: Wang, L. / Fu, T.-M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e6u.cif.gz | 940.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e6u.ent.gz | 775.8 KB | Display | PDB format |
PDBx/mmJSON format | 8e6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e6u_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 8e6u_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8e6u_validation.xml.gz | 156.1 KB | Display | |
Data in CIF | 8e6u_validation.cif.gz | 226.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/8e6u ftp://data.pdbj.org/pub/pdb/validation_reports/e6/8e6u | HTTPS FTP |
-Related structure data
Related structure data | 27926MC 8e6qC 8e6rC 8e6sC 8e6tC 8e6vC 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: 171416.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRPM2, EREG1, KNP3, LTRPC2, TRPC7 / Production host: Homo sapiens (human) / References: UniProt: O94759 #2: Chemical | ChemComp-UOZ / [( Mass: 619.412 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N5O13P2 / Feature type: SUBJECT OF INVESTIGATION 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: Human TRPM2 in 1 mM F-dADPR / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.75 mg/ml / 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 FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61503 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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