[English] 日本語
Yorodumi- PDB-4ilc: The GLIC pentameric ligand-gated ion channel in complex with sulfates -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ilc | ||||||
---|---|---|---|---|---|---|---|
Title | The GLIC pentameric ligand-gated ion channel in complex with sulfates | ||||||
Components | Proton-gated ion channel | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN / pentameric ligand-gated ion channel / ion channel / membrane | ||||||
Function / homology | Function and homology information sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Sauguet, L. / Malherbe, L. / Corringer, P.J. / Delarue, M. | ||||||
Citation | Journal: Embo J. / Year: 2013 Title: Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. Authors: Sauguet, L. / Poitevin, F. / Murail, S. / Van Renterghem, C. / Moraga-Cid, G. / Malherbe, L. / Thompson, A.W. / Koehl, P. / Corringer, P.J. / Baaden, M. / Delarue, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ilc.cif.gz | 334.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ilc.ent.gz | 272 KB | Display | PDB format |
PDBx/mmJSON format | 4ilc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/4ilc ftp://data.pdbj.org/pub/pdb/validation_reports/il/4ilc | HTTPS FTP |
---|
-Related structure data
Related structure data | 4hfiSC 4il4C 4il9C 4ilaC 4ilbC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 11 molecules ABCDE
#1: Protein | Mass: 36430.867 Da / Num. of mol.: 5 / Fragment: UNP residues 44-358 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C43 / References: UniProt: Q7NDN8 #6: Sugar | ChemComp-LMT / |
---|
-Non-polymers , 7 types, 86 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-PLC / #4: Chemical | ChemComp-UNL / Num. of mol.: 10 / Source method: obtained synthetically #5: Chemical | ChemComp-CL / #7: Chemical | ChemComp-NA / #8: Chemical | ChemComp-SO4 / #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.19 Å3/Da / Density % sol: 76.3 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 12-15% PEG 4K, 0.1M Na Acetate pH4, 0.2M NH4SO4, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→49.5 Å / Num. all: 75020 / Num. obs: 74893 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 83.34 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.054 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.99→3.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.6 / Num. unique all: 10804 / Rsym value: 0.346 / % possible all: 98.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HFI Resolution: 2.99→34.53 Å / Cor.coef. Fo:Fc: 0.8503 / Cor.coef. Fo:Fc free: 0.7841 / SU R Cruickshank DPI: 0.501 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.84 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.401 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→34.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.99→3.07 Å / Total num. of bins used: 20
|