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Yorodumi- PDB-1dp4: DIMERIZED HORMONE BINDING DOMAIN OF THE ATRIAL NATRIURETIC PEPTID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dp4 | |||||||||
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Title | DIMERIZED HORMONE BINDING DOMAIN OF THE ATRIAL NATRIURETIC PEPTIDE RECEPTOR | |||||||||
Components | ATRIAL NATRIURETIC PEPTIDE RECEPTOR A | |||||||||
Keywords | HORMONE/GROWTH FACTOR RECEPTOR / LYASE / periplasmic binding protein fold / dimer / LYASE COMPLEX / HORMONE-GROWTH FACTOR RECEPTOR | |||||||||
Function / homology | Function and homology information Physiological factors / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / hormone binding ...Physiological factors / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / hormone binding / adenylate cyclase activity / dopamine metabolic process / cGMP-mediated signaling / peptide hormone binding / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of blood pressure / receptor complex / cell surface receptor signaling pathway / protein kinase activity / intracellular signal transduction / GTP binding / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | |||||||||
Authors | van den Akker, F. / Zhang, X. / Miyagi, M. / Huo, X. / Misono, K.S. / Yee, V.C. | |||||||||
Citation | Journal: Nature / Year: 2000 Title: Structure of the dimerized hormone-binding domain of a guanylyl-cyclase-coupled receptor. Authors: van den Akker, F. / Zhang, X. / Miyagi, M. / Huo, X. / Misono, K.S. / Yee, V.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dp4.cif.gz | 188.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dp4.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dp4_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1dp4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1dp4_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 1dp4_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dp4 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dp4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | THE DIMER IN THIS ENTRY IS THE HEAD TO HEAD (HH)-DIMER THAT HAS SUBSEQUENTLY BEEN IDENTIFIED AS THE PHYSIOLOGICALLY ACTIVE DIMER BY SITE-DIRECTED MUTAGENESIS STUDIES (QIU, Y., OGAWA, H., ZHANG, X., MISONO, K.S. J.BIOL.CHEM. 279:6115-23, 2004) AND THE DIMER IN SOLUTION BY ELECTRON MICROSCOPY COUPLED WITH SINGLE PARTICLE RECONSTRUCTION (SUBMITTED FOR PUBLICATION). THE CC DIMER (biolomecule 1) WAS CHOSEN by author FOR A SLIGHTLY LARGER BURIED SURFACE AREA AND MORE CARBOXYL TERMINAL STRUCTURE ASSIGNED. |
-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 48434.828 Da / Num. of mol.: 2 / Fragment: HORMONE BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PCDNA3-NPR / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P18910, guanylate cyclase |
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-Sugars , 2 types, 5 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 525 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #6: 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: 2.99 Å3/Da / Density % sol: 58.92 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 80413 / Num. obs: 79776 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 4 % / Rmerge(I) obs: 0.285 / Num. unique all: 12036 / % possible all: 96.8 |
Reflection shell | *PLUS % possible obs: 96.8 % |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3501141.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.45 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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