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Yorodumi- PDB-7n5w: ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n5w | ||||||
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Title | ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing GGACCC (Oligo 23) | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / 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: 2.24 Å | ||||||
Authors | Horton, J.R. / Ren, R. / Cheng, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia. Authors: Ren, R. / Horton, J.R. / Chen, Q. / Yang, J. / Liu, B. / Huang, Y. / Blumenthal, R.M. / Zhang, X. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n5w.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n5w.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 7n5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n5w_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 7n5w_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 7n5w_validation.xml.gz | 7 KB | Display | |
Data in CIF | 7n5w_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/7n5w ftp://data.pdbj.org/pub/pdb/validation_reports/n5/7n5w | HTTPS FTP |
-Related structure data
Related structure data | 7n5uSC 7n5vC 8e3dC 8e3eC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 15424.003 Da / Num. of mol.: 1 / Fragment: zinc finger domain (UNP residues 380-500) 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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-DNA chain , 2 types, 2 molecules XY
#2: DNA chain | Mass: 4916.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#3: DNA chain | Mass: 4880.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 3 types, 42 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.16 Å3/Da / Density % sol: 61.05 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium malonate, pH 5.0, 12% PEG3350 |
-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: Apr 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→37.08 Å / Num. obs: 25580 / % possible obs: 89.5 % / Redundancy: 11.4 % / Biso Wilson estimate: 53.33 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.035 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.24→2.33 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1003 / CC1/2: 0.598 / Rpim(I) all: 0.47 / % possible all: 43.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7N5U Resolution: 2.24→37.08 Å / SU ML: 0.3644 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1111 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: 65.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→37.08 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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