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Yorodumi- PDB-7n5s: ZBTB7A Zinc Finger Domain Bound to -200 Site of Fetal Globin Prom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n5s | ||||||
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Title | ZBTB7A Zinc Finger Domain Bound to -200 Site of Fetal Globin Promoter (Oligo 6) | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Z=zinc-finger domain / gene expression / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information regulation of transcription regulatory region DNA binding / negative regulation of androgen receptor signaling pathway / DNA-dependent protein kinase complex / double-strand break repair via classical nonhomologous end joining / regulation of DNA-binding transcription factor activity / regulation of glycolytic process / nuclear androgen receptor binding / histone acetyltransferase binding / regulation of alternative mRNA splicing, via spliceosome / negative regulation of Notch signaling pathway ...regulation of transcription regulatory region DNA binding / negative regulation of androgen receptor signaling pathway / DNA-dependent protein kinase complex / double-strand break repair via classical nonhomologous end joining / regulation of DNA-binding transcription factor activity / regulation of glycolytic process / nuclear androgen receptor binding / histone acetyltransferase binding / regulation of alternative mRNA splicing, via spliceosome / negative regulation of Notch signaling pathway / fat cell differentiation / erythrocyte maturation / SMAD binding / protein localization to nucleus / B cell differentiation / transcription corepressor binding / negative regulation of transforming growth factor beta receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / chromatin organization / positive regulation of NF-kappaB transcription factor activity / site of double-strand break / DNA-binding transcription factor binding / regulation of apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
Authors | Horton, J.R. / Ren, R. / Cheng, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2021 Title: Structural basis for human ZBTB7A action at the fetal globin promoter. Authors: Yang, Y. / Ren, R. / Ly, L.C. / Horton, J.R. / Li, F. / Quinlan, K.G.R. / Crossley, M. / Shi, Y. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n5s.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n5s.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 7n5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n5s_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 7n5s_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 7n5s_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 7n5s_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/7n5s ftp://data.pdbj.org/pub/pdb/validation_reports/n5/7n5s | HTTPS FTP |
-Related structure data
Related structure data | 7eyiC 7n5tC 7n5uS S: Starting model for refinement C: citing same article (ref.) |
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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: Protein | Mass: 16638.525 Da / Num. of mol.: 1 / Fragment: zinc finger domain (UNP residues 369-500) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB7A, FBI1, LRF, ZBTB7, ZNF857A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: O95365 | ||||
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#2: DNA chain | Mass: 4676.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#3: DNA chain | Mass: 4506.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→36.32 Å / Num. obs: 10160 / % possible obs: 92.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 107.27 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.03 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.67 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 628 / CC1/2: 0.61 / Rpim(I) all: 0.701 / % possible all: 66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7N5U Resolution: 2.86→36.32 Å / SU ML: 0.4711 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.628 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.86→36.32 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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