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Yorodumi- PDB-1kb4: Crystal Structure of VDR DNA-binding Domain Bound to a Canonical ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kb4 | ||||||
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Title | Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / VDR / NUCLEAR RECEPTOR / PROTEIN-DNA COMPLEX / VITAMIN D / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / phosphate ion transmembrane transport / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / intracellular calcium ion homeostasis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / calcium ion transport / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Shaffer, P.L. / Gewirth, D.T. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Structural basis of VDR-DNA interactions on direct repeat response elements. Authors: Shaffer, P.L. / Gewirth, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kb4.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kb4.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 1kb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/1kb4 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/1kb4 | HTTPS FTP |
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-Related structure data
Related structure data | 1kb2C 1kb6C 2nllS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5534.607 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Canonical Direct Repeat with 3 Base Pair Spacer (DR3) Response Element | ||||
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#2: DNA chain | Mass: 5498.551 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Canonical Direct Repeat with 3 Base Pair Spacer (DR3) Response Element | ||||
#3: Protein | Mass: 12953.305 Da / Num. of mol.: 2 / Fragment: DNA-binding Domain (Residues 16-125) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VDR / Plasmid: PET11A-VDR-N1-RPLKS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11473 #4: Chemical | ChemComp-ZN / #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: 3.06 Å3/Da / Density % sol: 59.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å |
Detector | Type: APS-1 / Detector: CCD / Date: Sep 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 12384 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 79.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1173 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TR Half-Complex from PDB Entry 2NLL Resolution: 2.8→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 464135.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.5931 Å2 / ksol: 0.309478 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Num. reflection obs: 9350 / % reflection Rfree: 10 % / Rfactor obs: 0.214 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.486 / Rfactor Rwork: 0.472 / Rfactor obs: 0.472 |