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Yorodumi- PDB-1r1k: Crystal structure of the ligand-binding domains of the heterodime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r1k | ||||||
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Title | Crystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to ponasterone A | ||||||
Components |
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Keywords | hormone/growth factor receptor / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / HETERODIMER / ALPHA-HELICAL SANDWICH / Structural Proteomics in Europe / SPINE / Structural Genomics / hormone-growth factor receptor COMPLEX | ||||||
Function / homology | Function and homology information ecdysone binding / ecdysone receptor signaling pathway / bile acid signaling pathway / nuclear steroid receptor activity / negative regulation of inflammatory response / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II ...ecdysone binding / ecdysone receptor signaling pathway / bile acid signaling pathway / nuclear steroid receptor activity / negative regulation of inflammatory response / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Heliothis virescens (tobacco budworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Billas, I.M.L. / Iwema, T. / Garnier, J.-M. / Mitschler, A. / Rochel, N. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Nature / Year: 2003 Title: Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor. Authors: Billas, I.M.L. / Iwema, T. / Garnier, J.M. / Mitschler, A. / Rochel, N. / Moras, D. | ||||||
History |
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Remark 999 | sequence no suitable sequence database reference was available for chains A or D, at the time of ...sequence no suitable sequence database reference was available for chains A or D, at the time of processing this file |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r1k.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r1k.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r1k_validation.pdf.gz | 964.1 KB | Display | wwPDB validaton report |
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Full document | 1r1k_full_validation.pdf.gz | 995.2 KB | Display | |
Data in XML | 1r1k_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 1r1k_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r1k ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r1k | HTTPS FTP |
-Related structure data
Related structure data | 1r20C 1db1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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
#1: Protein | Mass: 30368.961 Da / Num. of mol.: 1 / Fragment: hormone binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Gene: ECR OR NR1H1 / Plasmid: pET32b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O18473 |
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#2: Protein | Mass: 29951.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Plasmid: pACYC11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIF6 |
#3: Chemical | ChemComp-P1A / |
#4: Chemical | ChemComp-EPH / |
#5: 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: 2.39 Å3/Da / Density % sol: 48.44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG 4000, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 28, 2002 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 13703 / Num. obs: 13703 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rsym value: 0.052 |
Reflection shell | Resolution: 2.9→2.97 Å / Rsym value: 0.38 / % possible all: 97.9 |
Reflection | *PLUS Redundancy: 9.5 % / Num. measured all: 129598 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 97.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Vitamin D receptor, PDB entry 1DB1 Resolution: 2.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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