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- PDB-1fd0: ISOTYPE SELECTIVITY OF THE HUMAN RETINOIC ACID NUCLEAR RECEPTOR H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fd0 | ||||||
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Title | ISOTYPE SELECTIVITY OF THE HUMAN RETINOIC ACID NUCLEAR RECEPTOR HRAR: THE COMPLEX WITH THE RARGAMMA-SELECTIVE RETINOID SR11254 | ||||||
![]() | RETINOIC ACID RECEPTOR GAMMA-1 | ||||||
![]() | GENE REGULATION / isotype selectivity / retinoid ligand complexes / drug design / antiparallel alpha-helical sandwich fold / CH...O hydrogen bond / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | ![]() 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 / cellular response to corticotropin-releasing hormone stimulus / nuclear glucocorticoid receptor binding / prostate gland epithelium morphogenesis ...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 / cellular response to corticotropin-releasing hormone stimulus / nuclear glucocorticoid receptor binding / 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 / face development / retinoic acid receptor signaling pathway / canonical Wnt signaling pathway / nuclear retinoid X receptor binding / cellular response to retinoic acid / response to retinoic acid / negative regulation of stem cell proliferation / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / stem cell proliferation / neural tube closure / multicellular organism growth / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / apoptotic process / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Klaholz, B.P. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: C-H...O hydrogen bonds in the nuclear receptor RARgamma--a potential tool for drug selectivity. Authors: Klaholz, B. / Moras, D. #1: ![]() 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. #2: ![]() 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. #3: ![]() Title: Crystal structure of the RARgamma ligand-binding domain bound to all-trans retinoic acid. Authors: Renaud, J.-P. / Rochel, N. / Vivat, V. / Chambon, P. / Gronemeyer, H. / Moras, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 53.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fcyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26535.070 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH SR11254, RESIDUE 254 / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-254 / |
#3: Sugar | ChemComp-LMU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % | ||||||||||||||||||||||||||||
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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 at 290K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 11, 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: 1.38→20 Å / Num. all: 59004 / Num. obs: 59004 / % possible obs: 99.8 % / Redundancy: 4.93 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.38→1.41 Å / Redundancy: 4 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3852 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 4.9 % / Num. measured all: 291021 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FCY Resolution: 1.38→6 Å / Num. parameters: 21188 / Num. restraintsaints: 26389 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.4%
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 1935 / Occupancy sum non hydrogen: 2200.2 | |||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→6 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / % reflection Rfree: 5 % / Rfactor all: 0.131 / Rfactor Rfree: 0.158 / Rfactor Rwork: 0.13 | |||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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