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Yorodumi- PDB-3lbd: LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lbd | ||||||
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Title | LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO 9-CIS RETINOIC ACID | ||||||
Components | RETINOIC ACID RECEPTOR GAMMA | ||||||
Keywords | NUCLEAR RECEPTOR / RETINOIC ACID RECEPTOR / ALL-TRANS RETINOIC ACID / LIGAND-BINDING DOMAIN / COMPLEX / HOLO FORM / TRANSCRIPTION REGULATION / LIGAND-DEPENDENT / ACTIVE CONFORMATION / 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 / 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 / stem cell proliferation / cellular response to leukemia inhibitory factor / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Klaholz, B.P. / Renaud, J.-P. / Mitschler, A. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Conformational adaptation of agonists to the human nuclear receptor RAR gamma. Authors: Klaholz, B.P. / Renaud, J.P. / Mitschler, A. / Zusi, C. / Chambon, P. / Gronemeyer, H. / Moras, D. #1: Journal: Nature / Year: 1995 Title: Crystal Structure of the Rar-Gamma Ligand-Binding Domain Bound to All-Trans Retinoic Acid Authors: Renaud, J.P. / Rochel, N. / Ruff, M. / Vivat, V. / Chambon, P. / Gronemeyer, H. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lbd.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lbd.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 3lbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lbd_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 3lbd_full_validation.pdf.gz | 439.7 KB | Display | |
Data in XML | 3lbd_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 3lbd_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/3lbd ftp://data.pdbj.org/pub/pdb/validation_reports/lb/3lbd | HTTPS FTP |
-Related structure data
Related structure data | 4lbdC 2lbdS S: Starting model for refinement C: citing same article (ref.) |
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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: 30193.055 Da / Num. of mol.: 1 / Fragment: LBD, LIGAND-BINDING DOMAIN, RESIDUES 178 - 423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: HRARGAMMA / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22932, UniProt: P13631*PLUS |
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#2: Chemical | ChemComp-9CR / ( |
#3: 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: 2.36 Å3/Da / Density % sol: 33 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. obs: 11390 / % possible obs: 98.45 % / Redundancy: 4.45 % / Rsym value: 0.074 / Net I/σ(I): 25.43 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 7.29 / Rsym value: 0.3 / % possible all: 97.8 |
Reflection | *PLUS Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 97.8 % / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: 2LBD Resolution: 2.4→5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters | Biso mean: 36.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→5 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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