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Yorodumi- PDB-1g2f: STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (TATAZF;CLONE #6) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2f | ||||||
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Title | STRUCTURE OF A CYS2HIS2 ZINC FINGER/TATA BOX COMPLEX (TATAZF;CLONE #6) | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / phage display / zinc finger-DNA complex / TATA box / Cys2His2 / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / : / positive regulation of smooth muscle cell migration / skeletal muscle cell differentiation / locomotor rhythm / T cell differentiation / estrous cycle / RNA polymerase II core promoter sequence-specific DNA binding / BMP signaling pathway / long-term memory / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / regulation of long-term neuronal synaptic plasticity / circadian regulation of gene expression / response to insulin / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of miRNA transcription / positive regulation of neuron apoptotic process / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / learning or memory / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Wolfe, S.A. / Grant, R.A. / Elrod-Erickson, M. / Pabo, C.O. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Authors: Wolfe, S.A. / Grant, R.A. / Elrod-Erickson, M. / Pabo, C.O. #1: Journal: Science / Year: 1997 Title: A General Strategy for Selecting High-Affinity Zinc Finger Proteins for Diverse DNA Target Sites Authors: Greisman, H.A. / Pabo, C.O. #2: Journal: Structure / Year: 1996 Title: Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions Authors: Elrod-Erickson, M. / Rould, M.A. / Nekludova, L. / Pabo, C.O. #3: Journal: J.Mol.Biol. / Year: 1999 Title: Analysis of Zinc Fingers Optimized via Phage Display: Evaluating the Utility of a Recognition Code Authors: Wolfe, S.A. / Greisman, H.A. / Ramm, E.I. / Pabo, C.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2f.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2f.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 1g2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2f ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 4980.269 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 4815.126 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 10632.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: PROTEIN SELECTED BY PHAGE DISPLAY; / Plasmid: PET21D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P08046 #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.02 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 400; NaCl; Bis-Tris Propane; CoCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.5418 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2000 / Details: KOHZU double crystal monochromator |
Radiation | Monochromator: KOHZU double crystal monochormator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 43331 / Num. obs: 43331 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.46 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 7.4 / Net I/σ(I): 28.52 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.14 % / Mean I/σ(I) obs: 6.58 / Num. unique all: 3595 / Rsym value: 56.7 / % possible all: 96.2 |
Reflection | *PLUS Num. measured all: 496779 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 96.2 % / Rmerge(I) obs: 0.567 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: Zif268 Resolution: 2→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 Stereochemistry target values: Xplor parameter set: param19.sol;parhcsdx.pro;dna-rna.param
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Displacement parameters | Biso mean: 41.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.233 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.376 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.365 |