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- PDB-4qc3: Crystal structure of human BAZ2B bromodomain in complex with a di... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qc3 | ||||||
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Title | Crystal structure of human BAZ2B bromodomain in complex with a diacetylated histone 4 peptide (H4K8acK12ac) | ||||||
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![]() | TRANSCRIPTION / Bromodomain adjacent to zinc finger domain protein 2B / hWALp4 / KIAA1476 / transcriptional regulation / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tallant, C. / Jose, B. / Picaud, S. / Chaikuad, A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Tallant, C. / Jose, B. / Picaud, S. / Chaikuad, A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.5 KB | Display | ![]() |
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PDB format | ![]() | 81.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.4 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lz2C ![]() 4q6fC ![]() 4qbmC ![]() 4qc1C ![]() 4qf2C ![]() 4qf3C ![]() 1dvvS ![]() 1x0jS ![]() 2grcS ![]() 2oo1S ![]() 2ossS ![]() 2uouS ![]() 3d7cS ![]() 3daiS ![]() 3dwyS ![]() 3g0lS ![]() 3hmhS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12489.299 Da / Num. of mol.: 2 / Fragment: unp residues 2062-2166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 699.798 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% PEG 8000, 0.2M calcium acetate, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→29.18 Å / Num. all: 30743 / Num. obs: 30743 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.062 Å2 / Rmerge(I) obs: 0.019 / Rsym value: 0.015 / Net I/σ(I): 45.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Ensemble of PDB ENTRY 3G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY Resolution: 1.6→29.179 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.298 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.082 / 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: 14.502 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.179 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.599→1.64 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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