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Yorodumi- PDB-8fcz: Crystal structure of ground-state rhodopsin in complex with a nanobody -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fcz | ||||||||||||
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Title | Crystal structure of ground-state rhodopsin in complex with a nanobody | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / TRANSMEMBRANE PROTEIN / GPCR / NANOBODY / RETINAL | ||||||||||||
Function / homology | Function and homology information Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : ...Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / phototransduction, visible light / thermotaxis / Activation of the phototransduction cascade / detection of temperature stimulus involved in thermoception / outer membrane / arrestin family protein binding / photoreceptor cell maintenance / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Lama glama (llama) Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||||||||
Authors | Salom, D. / Palczewski, K. / Kiser, P.D. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain. Authors: Wu, A. / Salom, D. / Hong, J.D. / Tworak, A. / Watanabe, K. / Pardon, E. / Steyaert, J. / Kandori, H. / Katayama, K. / Kiser, P.D. / Palczewski, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fcz.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fcz.ent.gz | 145.5 KB | Display | PDB format |
PDBx/mmJSON format | 8fcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/8fcz ftp://data.pdbj.org/pub/pdb/validation_reports/fc/8fcz | HTTPS FTP |
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-Related structure data
Related structure data | 8fd0C 8fd1C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Antibody / Non-polymers , 3 types, 6 molecules ABCD
#1: Protein | Mass: 39031.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02699 #2: Antibody | Mass: 13849.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #7: Chemical | |
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-Sugars , 4 types, 4 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 |
#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.93 Å3/Da / Density % sol: 75.03 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 30% PEG 600 0.1 M Tricine pH 8 1.2 mM F3215-0002 2% IPTG 50 mM phenol 5 mM EDTA 5 mM beta mercaptoethanol 50 mM Cyglu-4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→50 Å / Num. obs: 20570 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.22 |
Reflection shell | Resolution: 3.7→3.92 Å / Rmerge(I) obs: 2.831 / Mean I/σ(I) obs: 0.71 / Num. unique obs: 3236 / CC1/2: 0.378 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→49.76 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.862 / SU B: 55.867 / SU ML: 0.718 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.741 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 349.79 Å2 / Biso mean: 211.193 Å2 / Biso min: 153.52 Å2
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Refinement step | Cycle: final / Resolution: 3.7→49.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.701→3.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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