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Yorodumi- PDB-8d51: Parathyroid hormone 1 receptor extracellular domain complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d51 | ||||||
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Title | Parathyroid hormone 1 receptor extracellular domain complexed with a peptide ligand containing beta-3-homotryptophan | ||||||
Components |
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Keywords | SIGNALING PROTEIN / parathyroid hormone 1 receptor / signaling / beta-amino acid | ||||||
Function / homology | Function and homology information negative regulation of chondrocyte development / regulation of chondrocyte differentiation / parathyroid hormone receptor activity / cAMP metabolic process / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / parathyroid hormone receptor activity / cAMP metabolic process / G protein-coupled peptide receptor activity / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding / bone mineralization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / peptide hormone binding / epidermis development / chondrocyte differentiation / cell maturation / bone resorption / skeletal system development / female pregnancy / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / intracellular calcium ion homeostasis / : / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / regulation of gene expression / basolateral plasma membrane / cell population proliferation / in utero embryonic development / cell surface receptor signaling pathway / receptor complex / apical plasma membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yu, Z. / Kreitler, D.F. / Gellman, S.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification. Authors: Yu, Z. / Kreitler, D.F. / Chiu, Y.T.T. / Xu, R. / Bruchs, A.T. / Bingman, C.A. / Gellman, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d51.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d51.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 8d51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/8d51 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d51 | HTTPS FTP |
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-Related structure data
Related structure data | 8d52C 3h3gS S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11995.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTH1R, PTHR, PTHR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03431 |
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#2: Protein/peptide | Mass: 2822.272 Da / Num. of mol.: 1 / Mutation: I31 substituted with beta-3-tryptophan / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P12272 |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 28 % v/v PEG Smear Low, 0.1 M tris-HCl pH 8, 0.15 M Sodium citrate, 1% ethylene glycol, 1 mM ZnSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2022 / Details: KB |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920105 Å / Relative weight: 1 |
Reflection | Resolution: 1.997→49.179 Å / Num. obs: 7236 / % possible obs: 75.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 53.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Rrim(I) all: 0.063 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.997→2.206 Å / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 362 / CC1/2: 0.843 / Rpim(I) all: 0.628 / Rrim(I) all: 0.947 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H3G Resolution: 2→36.14 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.5025 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→36.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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