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Yorodumi- PDB-6fj3: High resolution crystal structure of parathyroid hormone 1 recept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fj3 | |||||||||
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Title | High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist. | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / GPCR / cell signalling / 7TM | |||||||||
Function / homology | Function and homology information : / type 1 parathyroid hormone receptor binding / parathyroid hormone receptor binding / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / parathyroid hormone receptor activity / positive regulation of cell proliferation in bone marrow / magnesium ion homeostasis / positive regulation of signal transduction / glycogen (starch) synthase activity ...: / type 1 parathyroid hormone receptor binding / parathyroid hormone receptor binding / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / parathyroid hormone receptor activity / positive regulation of cell proliferation in bone marrow / magnesium ion homeostasis / positive regulation of signal transduction / glycogen (starch) synthase activity / : / phosphate ion homeostasis / G protein-coupled peptide receptor activity / 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 / negative regulation of calcium ion transport / activation of phospholipase C activity / positive regulation of glycogen biosynthetic process / chondrocyte differentiation / positive regulation of bone mineralization / homeostasis of number of cells within a tissue / cell maturation / bone resorption / skeletal system development / positive regulation of glucose import / 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 / 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 / nucleotide binding / negative regulation of gene expression / positive regulation of cell population proliferation / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Pyrococcus abyssi (archaea) Equus caballus (horse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Ehrenmann, J. / Schoppe, J. / Klenk, C. / Rappas, M. / Kummer, L. / Dore, A.S. / Pluckthun, A. | |||||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2018 Title: High-resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist. Authors: Ehrenmann, J. / Schoppe, J. / Klenk, C. / Rappas, M. / Kummer, L. / Dore, A.S. / Pluckthun, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fj3.cif.gz | 281.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fj3.ent.gz | 223.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/6fj3 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/6fj3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 68389.203 Da / Num. of mol.: 1 Mutation: Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, ...Mutation: Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Gene: PTH1R, PTHR, PTHR1, PAB2292 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03431, UniProt: Q9V2J8 |
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#2: Protein/peptide | Mass: 4277.009 Da / Num. of mol.: 1 / Mutation: N41Q, G43A, H45W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: PTH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q27IM2 |
-Sugars , 4 types, 6 molecules
#3: 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)-[alpha-L-fucopyranose-(1-6)]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)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: Sugar |
-Non-polymers , 5 types, 168 molecules
#7: Chemical | ChemComp-OLA / #8: Chemical | ChemComp-ACY / | #9: Chemical | ChemComp-PG4 / | #10: Chemical | ChemComp-CL / | #11: Water | ChemComp-HOH / | |
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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: 3.47 Å3/Da / Density % sol: 64.53 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 0.1 M sodium citrate pH 6.0, 0.3 M sodium acetate, 31% PEG400, 20 uM E-PTH(1-34) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2017 |
Radiation | Monochromator: LN2 cooled fixed exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.39 Å / Num. obs: 33759 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 50.93 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.103 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.662 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3825 / CC1/2: 0.501 / Rpim(I) all: 1.214 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EE7, 3C4M Resolution: 2.5→49.386 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.386 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 |
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