+Open data
-Basic information
Entry | Database: PDB / ID: 5en0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of T94I rhodopsin mutant | |||||||||
Components |
| |||||||||
Keywords | SIGNALING PROTEIN / Rhodopsin / G protein-coupled receptors / Congenital stationary night blindness / constitutive activity | |||||||||
Function / homology | Function and homology information Adenylate cyclase inhibitory pathway / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / sensory perception of umami taste / absorption of visible light / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) ...Adenylate cyclase inhibitory pathway / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / sperm head plasma membrane / sensory perception of umami taste / absorption of visible light / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / The canonical retinoid cycle in rods (twilight vision) / sensory perception of sweet taste / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / 11-cis retinal binding / G protein-coupled photoreceptor activity / rod photoreceptor outer segment / detection of chemical stimulus involved in sensory perception of bitter taste / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / response to light intensity / Activation of the phototransduction cascade / phototransduction, visible light / outer membrane / detection of temperature stimulus involved in thermoception / photoreceptor cell maintenance / arrestin family protein binding / ADP signalling through P2Y purinoceptor 12 / Extra-nuclear estrogen signaling / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / response to light stimulus / sperm midpiece / visual perception / photoreceptor inner segment / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / microtubule cytoskeleton organization / heterotrimeric G-protein complex / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP binding / zinc ion binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | |||||||||
Authors | Singhal, A. / Guo, Y. / Matkovic, M. / Schertler, G. / Deupi, X. / Yan, E. / Standfuss, J. | |||||||||
Citation | Journal: Embo Rep. / Year: 2016 Title: Structural role of the T94I rhodopsin mutation in congenital stationary night blindness. Authors: Singhal, A. / Guo, Y. / Matkovic, M. / Schertler, G. / Deupi, X. / Yan, E.C. / Standfuss, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5en0.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5en0.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 5en0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/5en0 ftp://data.pdbj.org/pub/pdb/validation_reports/en/5en0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5dysC 4a4mS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 39046.641 Da / Num. of mol.: 1 / Mutation: N2C, T94I, D282C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RHO / Plasmid: pCMV-tet O / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: P02699 |
---|---|
#2: Protein/peptide | Mass: 1261.487 Da / Num. of mol.: 1 / Fragment: UNP residues 344-354 / Source method: obtained synthetically Details: GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-3 peptide Source: (synth.) Bos taurus (cattle) / References: UniProt: P0C7Q4*PLUS |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#6: Sugar |
-Non-polymers , 5 types, 31 molecules
#4: Chemical | ChemComp-RET / Mass: 284.436 Da / Num. of mol.: 1 / Mutation: N2C, T94I, D282C Source method: isolated from a genetically manipulated source Formula: C20H28O / Source: (gene. exp.) Bos taurus (cattle) / Gene: RHO / Plasmid: pCMV-tet O / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) | ||||||
---|---|---|---|---|---|---|---|
#5: Chemical | #7: Chemical | #8: Chemical | ChemComp-SO4 / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, Sodium acetate / PH range: 4-6 |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 30386 / % possible obs: 99.5 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.722 / % possible all: 97.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A4M Resolution: 2.81→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.623 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.989 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.81→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|