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Yorodumi- PDB-1exa: ENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF TH... -
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-Basic information
Entry | Database: PDB / ID: 1exa | ||||||
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Title | ENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF THE HUMAN RETINOIC ACID RECEPTOR HRARGAMMA LIGAND BINDING DOMAIN: THE COMPLEX WITH THE ACTIVE R-ENANTIOMER BMS270394. | ||||||
Components | RETINOIC ACID RECEPTOR GAMMA-2 | ||||||
Keywords | GENE REGULATION / enantiomer discrimination / retinoid ligand complexes / antiparallel alpha-helical sandwich fold / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | Function and homology information Harderian gland development / regulation of myeloid cell differentiation / growth plate cartilage chondrocyte growth / trachea cartilage development / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / positive regulation of programmed cell death / negative regulation of chondrocyte differentiation ...Harderian gland development / regulation of myeloid cell differentiation / growth plate cartilage chondrocyte growth / trachea cartilage development / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / positive regulation of programmed cell death / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / regulation of myelination / Signaling by Retinoic Acid / regulation of cell size / retinoic acid receptor signaling pathway / face development / nuclear retinoid X receptor binding / canonical Wnt signaling pathway / hormone-mediated signaling pathway / response to retinoic acid / negative regulation of stem cell proliferation / cellular response to retinoic acid / stem cell proliferation / cellular response to leukemia inhibitory factor / neural tube closure / Nuclear Receptor transcription pathway / multicellular organism growth / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of apoptotic process / negative regulation of cell population proliferation / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Klaholz, B.P. / Mitschler, A. / Belema, M. / Zusi, C. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRARgamma. Authors: Klaholz, B.P. / Mitschler, A. / Belema, M. / Zusi, C. / Moras, D. #1: Journal: Nat.Struct.Biol. / Year: 1998 Title: Conformational adaptation of agonists to the human nuclear receptor hRARgamma. Authors: Klaholz, B.P. / Renaud, J.-P. / Mitschler, A. / Zusi, C. / Chambon, P. / Gronemeyer, H. / Moras, D. #2: Journal: To be Published / Year: 2000 Title: Structural basis for isotype selectivity of the human retinoic acid nuclear receptor. Authors: Klaholz, B.P. / Mitschler, A. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1exa.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1exa.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 1exa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1exa_validation.pdf.gz | 919 KB | Display | wwPDB validaton report |
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Full document | 1exa_full_validation.pdf.gz | 924.8 KB | Display | |
Data in XML | 1exa_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 1exa_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/1exa ftp://data.pdbj.org/pub/pdb/validation_reports/ex/1exa | HTTPS FTP |
-Related structure data
Related structure data | 1exxC 4lbdS 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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Unit cell |
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-Components
#1: Protein | Mass: 27890.498 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: P22932, UniProt: P13631*PLUS |
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#2: Chemical | ChemComp-394 / |
#3: Sugar | ChemComp-LMU / |
#4: 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: 2.14 Å3/Da / Density % sol: 41.94 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal grow | *PLUS Temperature: 17 ℃ |
Components of the solutions | *PLUS Chemical formula: NaOAc |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 3, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→15 Å / Num. all: 37688 / Num. obs: 37688 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 1738 / Rsym value: 0.308 / % possible all: 91.2 |
Reflection | *PLUS Num. measured all: 131831 |
Reflection shell | *PLUS % possible obs: 91.2 % / Rmerge(I) obs: 0.308 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LBD Resolution: 1.59→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.59→15 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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