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- PDB-4lbd: LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lbd | ||||||
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Title | LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO THE SYNTHETIC AGONIST BMS961 | ||||||
![]() | RETINOIC ACID RECEPTOR GAMMA | ||||||
![]() | 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 | ![]() 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 / face development / canonical Wnt signaling pathway / retinoic acid receptor signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / negative regulation of stem cell proliferation / cellular response to retinoic acid / hormone-mediated signaling pathway / stem cell proliferation / cellular response to leukemia inhibitory factor / neural tube closure / multicellular organism growth / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Klaholz, B.P. / Renaud, J.-P. / Mitschler, A. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.9 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3lbdC ![]() 2lbdS S: Starting model for refinement C: citing same article ( |
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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: 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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-961 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() |
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: 2.5→14.97 Å / Num. obs: 9894 / % possible obs: 95.36 % / Redundancy: 2.98 % / Rsym value: 0.096 / Net I/σ(I): 15.28 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.67 / Rsym value: 0.32 / % possible all: 97.3 |
Reflection | *PLUS Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 97.3 % / Rmerge(I) obs: 0.32 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2LBD Resolution: 2.5→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: 37.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→5 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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