+Open data
-Basic information
Entry | Database: PDB / ID: 7wdb | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human TRPC5 channel in complex with riluzole | |||||||||||||||
Components | Short transient receptor potential channel 5 | |||||||||||||||
Keywords | MEMBRANE PROTEIN / TRPC5 / riluzole / activator | |||||||||||||||
Function / homology | Function and homology information regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / actinin binding / TRP channels / clathrin binding ...regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / actinin binding / TRP channels / clathrin binding / positive regulation of axon extension / regulation of cytosolic calcium ion concentration / calcium channel complex / positive regulation of neuron differentiation / positive regulation of peptidyl-threonine phosphorylation / calcium ion transmembrane transport / calcium channel activity / neuron differentiation / calcium ion transport / ATPase binding / nervous system development / actin binding / positive regulation of cytosolic calcium ion concentration / growth cone / neuron apoptotic process / neuronal cell body / positive regulation of cell population proliferation / dendrite / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||||||||
Authors | Chen, L. / Wei, M. / Yang, Y. | |||||||||||||||
Funding support | China, 4items
| |||||||||||||||
Citation | Journal: Cell Discov / Year: 2022 Title: Structural identification of riluzole-binding site on human TRPC5. Authors: Yaxiong Yang / Miao Wei / Lei Chen / | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7wdb.cif.gz | 538 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7wdb.ent.gz | 451.5 KB | Display | PDB format |
PDBx/mmJSON format | 7wdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wdb_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7wdb_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7wdb_validation.xml.gz | 80.7 KB | Display | |
Data in CIF | 7wdb_validation.cif.gz | 112 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/7wdb ftp://data.pdbj.org/pub/pdb/validation_reports/wd/7wdb | HTTPS FTP |
-Related structure data
Related structure data | 32436MC 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 88848.578 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC5, TRP5 / Production host: Homo sapiens (human) / References: UniProt: Q9UL62 |
---|
-Non-polymers , 7 types, 28 molecules
#2: Chemical | ChemComp-POV / ( #3: Chemical | ChemComp-Y01 / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-657 / #7: Chemical | ChemComp-PTY / #8: Chemical | ChemComp-7OC / [ |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human transient receptor potential channel 5 tetramer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
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 |
---|---|
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: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175028 / Symmetry type: POINT |