+Open data
-Basic information
Entry | Database: PDB / ID: 1jdn | |||||||||
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Title | Crystal Structure of Hormone Receptor | |||||||||
Components | ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR | |||||||||
Keywords | SIGNALING PROTEIN / Natriuretic peptide receptor / dimer / allosteric activation | |||||||||
Function / homology | Function and homology information natriuretic peptide receptor activity / osteoclast proliferation / hormone binding / positive regulation of urine volume / regulation of osteoblast proliferation / G protein-coupled peptide receptor activity / negative regulation of cold-induced thermogenesis / chloride ion binding / peptide hormone binding / blood vessel remodeling ...natriuretic peptide receptor activity / osteoclast proliferation / hormone binding / positive regulation of urine volume / regulation of osteoblast proliferation / G protein-coupled peptide receptor activity / negative regulation of cold-induced thermogenesis / chloride ion binding / peptide hormone binding / blood vessel remodeling / skeletal system development / positive regulation of nitric-oxide synthase activity / response to ischemia / peptide binding / regulation of blood pressure / angiogenesis / signal transduction / protein homodimerization activity / protein-containing complex / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | He, X.-L. / Chow, D.-C. / Martick, M.M. / Garcia, K.C. | |||||||||
Citation | Journal: Science / Year: 2001 Title: Allosteric activation of a spring-loaded natriuretic peptide receptor dimer by hormone. Authors: He, X.l. / Chow, D.c. / Martick, M.M. / Garcia, K.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jdn.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jdn.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jdn ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jdn | 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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Details | The second part of the biological assembly is generated by the two fold axis: -y, -x, -z+5/6. |
-Components
#1: Protein | Mass: 49541.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P17342 |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D- ...beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-4)-alpha-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: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: potassium sodium phosphate, lithium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
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Crystal grow | *PLUS Method: other |
Components of the solutions | *PLUS Conc.: 1.5 M / Common name: sodium potassium phosphate / Details: or potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 43722 / Num. obs: 43722 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 86.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2 / % possible all: 98.4 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 217841 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.435 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The complex of this receptor with hormone being processed presently. Resolution: 2.9→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 65.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.03
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.243 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 65.8 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Rfactor Rfree: 0.389 / Rfactor Rwork: 0.367 |