[English] 日本語
![](img/lk-miru.gif)
- PDB-6fj3: High resolution crystal structure of parathyroid hormone 1 recept... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6fj3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist. | |||||||||
![]() |
| |||||||||
![]() | MEMBRANE PROTEIN / GPCR / cell signalling / 7TM | |||||||||
Function / homology | ![]() : / 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) / glycogen biosynthetic process / osteoblast development / peptide hormone receptor binding / positive regulation of inositol phosphate biosynthetic process / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of calcium ion transport / : / positive regulation of glycogen biosynthetic process / chondrocyte differentiation / positive regulation of bone mineralization / cell maturation / homeostasis of number of cells within a tissue / 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 / in utero embryonic development / cell population proliferation / cell surface receptor signaling pathway / receptor complex / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / 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 / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ehrenmann, J. / Schoppe, J. / Klenk, C. / Rappas, M. / Kummer, L. / Dore, A.S. / Pluckthun, A. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 281.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 223.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() Gene: PTH1R, PTHR, PTHR1, PAB2292 / Strain: GE5 / Orsay / Production host: ![]() ![]() |
---|---|
#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.) ![]() ![]() ![]() ![]() |
-Sugars , 4 types, 6 molecules ![](data/chem/img/MAN.gif)
#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 |
---|---|
#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 ![](data/chem/img/OLA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-OLA / #8: Chemical | ChemComp-ACY / | #9: Chemical | ChemComp-PG4 / | #10: Chemical | ChemComp-CL / | #11: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.53 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|