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Yorodumi- PDB-3h3g: Crystal structure of the extracellular domain of the human parath... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h3g | |||||||||
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Title | Crystal structure of the extracellular domain of the human parathyroid hormone receptor (PTH1R) in complex with parathyroid hormone-related protein (PTHrP) | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / GPCR / extracellular domain / PTHrP / PTH / PTHR1 / Sugar transport / Transport / Hormone | |||||||||
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 / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process ...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 / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process / detection of maltose stimulus / maltose transport complex / bone mineralization / carbohydrate transport / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / epidermis development / chondrocyte differentiation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cell maturation / bone resorption / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / G alpha (s) signalling events / regulation of gene expression / basolateral plasma membrane / in utero embryonic development / cell population proliferation / periplasmic space / cell surface receptor signaling pathway / receptor complex / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / DNA damage response / positive regulation of cell population proliferation / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | |||||||||
Authors | Pioszak, A.A. / Xu, H.E. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural basis for parathyroid hormone-related protein binding to the parathyroid hormone receptor and design of conformation-selective peptides. Authors: Pioszak, A.A. / Parker, N.R. / Gardella, T.J. / Xu, H.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h3g.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h3g.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 3h3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h3g_validation.pdf.gz | 869 KB | Display | wwPDB validaton report |
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Full document | 3h3g_full_validation.pdf.gz | 873 KB | Display | |
Data in XML | 3h3g_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 3h3g_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/3h3g ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h3g | HTTPS FTP |
-Related structure data
Related structure data | 3c4mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 60297.941 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: b4034, JW3994, malE, PTHR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q03431 |
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#2: Protein/peptide | Mass: 2764.239 Da / Num. of mol.: 1 / Fragment: residues 12-34 / Source method: obtained synthetically / References: UniProt: P12272 |
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 7.5% PEG 2000, 13% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 40884 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 17 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.66 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.25 / % possible all: 55 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3C4M Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.784 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.155 / 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 max: 68.37 Å2 / Biso mean: 44.976 Å2 / Biso min: 28.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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