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Open data
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Basic information
Entry | Database: PDB / ID: 5en0 | |||||||||
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Title | Crystal Structure of T94I rhodopsin mutant | |||||||||
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![]() | SIGNALING PROTEIN / Rhodopsin / G protein-coupled receptors / Congenital stationary night blindness / constitutive activity | |||||||||
Function / homology | ![]() Adenylate cyclase inhibitory pathway / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / sensory perception of umami taste / absorption of visible light / Sensory perception of sweet, bitter, and umami (glutamate) taste ...Adenylate cyclase inhibitory pathway / Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / rod photoreceptor outer segment / 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 / : / photoreceptor inner segment membrane / podosome assembly / G protein-coupled opsin signaling pathway / 11-cis retinal binding / G protein-coupled photoreceptor activity / 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 / 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Singhal, A. / Guo, Y. / Matkovic, M. / Schertler, G. / Deupi, X. / Yan, E. / Standfuss, J. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.7 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dysC ![]() 4a4mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() |
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#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.) ![]() ![]() |
-Sugars , 2 types, 3 molecules ![](data/chem/img/BOG.gif)
#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 |
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#6: Sugar |
-Non-polymers , 5 types, 31 molecules ![](data/chem/img/RET.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PLM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-RET / ![]() Source method: isolated from a genetically manipulated source Formula: C20H28O / Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#5: Chemical | #7: Chemical | #8: Chemical | ChemComp-SO4 / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, Sodium acetate / PH range: 4-6 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: 1 / Resolution: 2.81→30 Å
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