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Yorodumi- PDB-4qf3: Crystal structure of human BAZ2B PHD zinc finger in the free form -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qf3 | ||||||
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Title | Crystal structure of human BAZ2B PHD zinc finger in the free form | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
Keywords | TRANSCRIPTION / Bromodomain adjacent to zinc finger domain protein 2B / KIAA1476 / transcriptional regulation interacting with ISWI | ||||||
Function / homology | Function and homology information chromatin remodeling / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Tallant, C. / Van Molle, I. / Chirgadze, D.Y. / Ciulli, A. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC. Authors: Cynthia Tallant / Erica Valentini / Oleg Fedorov / Lois Overvoorde / Fleur M Ferguson / Panagis Filippakopoulos / Dmitri I Svergun / Stefan Knapp / Alessio Ciulli / Abstract: Binding of the chromatin remodeling complex NoRC to RNA complementary to the rDNA promoter mediates transcriptional repression. TIP5, the largest subunit of NoRC, is involved in recruitment to rDNA ...Binding of the chromatin remodeling complex NoRC to RNA complementary to the rDNA promoter mediates transcriptional repression. TIP5, the largest subunit of NoRC, is involved in recruitment to rDNA by interactions with promoter-bound TTF-I, pRNA, and acetylation of H4K16. TIP5 domains that recognize posttranslational modifications on histones are essential for recruitment of NoRC to chromatin, but how these reader modules recognize site-specific histone tails has remained elusive. Here, we report crystal structures of PHD zinc finger and bromodomains from human TIP5 and BAZ2B in free form and bound to H3 and/or H4 histones. PHD finger functions as an independent structural module in recognizing unmodified H3 histone tails, and the bromodomain prefers H3 and H4 acetylation marks followed by a key basic residue, KacXXR. Further low-resolution analyses of PHD-bromodomain modules provide molecular insights into their trans histone tail recognition, required for nucleosome recruitment and transcriptional repression of the NoRC complex. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qf3.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qf3.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 4qf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qf3_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 4qf3_full_validation.pdf.gz | 422.4 KB | Display | |
Data in XML | 4qf3_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 4qf3_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/4qf3 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/4qf3 | HTTPS FTP |
-Related structure data
Related structure data | 4lz2C 4q6fC 4qbmC 4qc1C 4qc3C 4qf2C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 6543.708 Da / Num. of mol.: 2 / Fragment: unp residues 1928-1983 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q9UIF8 #2: Chemical | ChemComp-ZN / #3: 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: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 2.2M Na/K phosphate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.2816 Å | |||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2012 | |||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2816 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→29.41 Å / Num. all: 15620 / Num. obs: 14800 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.029 / Rsym value: 0.029 / Net I/σ(I): 29.7 | |||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 8.4 % / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: Arp/warp autobuilding model Resolution: 1.6→26.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.057 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.602→1.644 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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