[English] 日本語
Yorodumi- PDB-6m85: Crystal Structure of Inward Rectifier Kir2.2 in a different salt ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m85 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Inward Rectifier Kir2.2 in a different salt condition | |||||||||
Components | ATP-sensitive inward rectifier potassium channel 12 | |||||||||
Keywords | METAL TRANSPORT / Kir 2.2 | |||||||||
Function / homology | Function and homology information Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization ...Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | |||||||||
Authors | Lee, S.-J. / Nichols, C.G. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: J.Gen.Physiol. / Year: 2020 Title: Atomistic basis of opening and conduction in mammalian inward rectifier potassium (Kir2.2) channels. Authors: Zangerl-Plessl, E.M. / Lee, S.J. / Maksaev, G. / Bernsteiner, H. / Ren, F. / Yuan, P. / Stary-Weinzinger, A. / Nichols, C.G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6m85.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6m85.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 6m85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m85_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6m85_full_validation.pdf.gz | 439.9 KB | Display | |
Data in XML | 6m85_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6m85_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/6m85 ftp://data.pdbj.org/pub/pdb/validation_reports/m8/6m85 | HTTPS FTP |
-Related structure data
Related structure data | 6m84C 3spcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 39361.723 Da / Num. of mol.: 1 / Fragment: residues 38-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: KCNJ12 / Plasmid: pPicZ / Production host: Komagataella pastoris (fungus) / References: UniProt: F1NHE9 | ||
---|---|---|---|
#2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.35 Å3/Da / Density % sol: 71.7 % / Mosaicity: 0.658 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: evaporation / Details: PEG400, Trisodium Citrate, Tris / PH range: 7.1-7.4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2017 / Details: LR-Design detector positioner | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 17592 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Χ2: 1.037 / Net I/σ(I): 11.7 / Num. measured all: 114715 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SPC Resolution: 2.71→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.445 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.408 / ESU R Free: 0.277 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 197.64 Å2 / Biso mean: 107.846 Å2 / Biso min: 65.71 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.71→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.71→2.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|