+Open data
-Basic information
Entry | Database: PDB / ID: 8e6r | ||||||
---|---|---|---|---|---|---|---|
Title | Human TRPM2 ion channel in 1 mM 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 / TRP channels ...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 / TRP channels / dendritic cell chemotaxis / sodium channel activity / response to hydroperoxide / calcium ion transmembrane import into cytosol / 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: 5.6 Å | ||||||
Authors | Wang, L. / Fu, T.M. / Xia, S. / Wu, H. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: A unified mechanism for human TRPM2 activation, desensitization and inhibition Authors: Wang, L. / Fu, T.-M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8e6r.cif.gz | 931 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8e6r.ent.gz | 763.4 KB | Display | PDB format |
PDBx/mmJSON format | 8e6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e6r_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8e6r_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8e6r_validation.xml.gz | 160.5 KB | Display | |
Data in CIF | 8e6r_validation.cif.gz | 233.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/8e6r ftp://data.pdbj.org/pub/pdb/validation_reports/e6/8e6r | HTTPS FTP |
-Related structure data
Related structure data | 27923MC 8e6qC 8e6sC 8e6tC 8e6uC 8e6vC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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-APR / #3: Chemical | ChemComp-AR6 / [( Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human TRPM2 in 1 mM ADPR / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
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 |
---|---|
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: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86858 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|