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- PDB-5k5i: Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k5i | ||||||
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Title | Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P65 | ||||||
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![]() | TRANSCRIPTION/DNA / CCCTC-binding factor / CTCF / zinc finger / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() chromatin loop anchoring activity / chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region / condensed chromosome / epigenetic regulation of gene expression ...chromatin loop anchoring activity / chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region / condensed chromosome / epigenetic regulation of gene expression / male germ cell nucleus / transcription coregulator binding / chromosome segregation / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hashimoto, H. / Cheng, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Authors: Hashimoto, H. / Wang, D. / Horton, J.R. / Zhang, X. / Corces, V.G. / Cheng, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.6 KB | Display | ![]() |
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PDB format | ![]() | 35.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5k5hC ![]() 5k5jC ![]() 5k5lC ![]() 5kkqC ![]() 5t00C ![]() 5t0uC ![]() 5undC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13722.850 Da / Num. of mol.: 1 / Fragment: unp residues 378-489 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3888.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4057.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 16 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% (w/v) polyethylene glycol 3350, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 9, 2015 |
Radiation | Monochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27046 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→23.247 Å / Num. obs: 30205 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / CC1/2: 0.806 / Rmerge(I) obs: 0.105 / Net I/σ(I): 19.29 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.333 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→23.247 Å
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Refine LS restraints |
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LS refinement shell |
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