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Yorodumi- PDB-8gn3: The crystal structure of ZBTB10 ZF1-2 in complex with telomeric v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gn3 | ||||||
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Title | The crystal structure of ZBTB10 ZF1-2 in complex with telomeric vairant repeat TTGGGG | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Telomeric DNA binding / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information telomeric DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / chromosome, telomeric region / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Li, F.D. / Wang, S.M. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Structural insights into the recognition of telomeric variant repeat TTGGGG by broad-complex, tramtrack and bric-a-brac - zinc finger protein ZBTB10. Authors: Wang, S. / Xu, Z. / Li, M. / Lv, M. / Shen, S. / Shi, Y. / Li, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gn3.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gn3.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 8gn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gn3_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 8gn3_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 8gn3_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 8gn3_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/8gn3 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/8gn3 | HTTPS FTP |
-Related structure data
Related structure data | 8gn4C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 7991.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB10, RINZF, RINZFC / Production host: Escherichia coli (E. coli) / References: UniProt: Q96DT7 #2: DNA chain | Mass: 3435.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | Mass: 3271.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | 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: 2.08 Å3/Da / Density % sol: 40.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium HEPES, pH 8.2, 40 % v/v PEG 500 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→40 Å / Num. obs: 23647 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.063 / Χ2: 0.928 / Net I/σ(I): 6.9 / Num. measured all: 297558 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.8→33.08 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML
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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 max: 57.22 Å2 / Biso mean: 23.5228 Å2 / Biso min: 6.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→33.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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