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- PDB-2vpb: Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vpb | ||||||
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Title | Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex | ||||||
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![]() | GENE REGULATION / WNT SIGNALING PATHWAY / WNT SIGNALING COMPLEX / CHROMOSOMAL REARRANGEMENT / SIGNALING PROTEIN / BCL9 HD1 DOMAIN / HPYGO1 PHD DOMAIN / PROTO-ONCOGENE / PHOSPHOPROTEIN / HISTONE H3K4ME2 / ZINC / NUCLEUS / ZINC-FINGER / METAL-BINDING | ||||||
Function / homology | ![]() myotube differentiation involved in skeletal muscle regeneration / spermatid nucleus differentiation / beta-catenin-TCF complex / cis-Golgi network / myoblast differentiation / skeletal muscle cell differentiation / somatic stem cell population maintenance / protein localization to nucleus / sarcoplasm / canonical Wnt signaling pathway ...myotube differentiation involved in skeletal muscle regeneration / spermatid nucleus differentiation / beta-catenin-TCF complex / cis-Golgi network / myoblast differentiation / skeletal muscle cell differentiation / somatic stem cell population maintenance / protein localization to nucleus / sarcoplasm / canonical Wnt signaling pathway / hematopoietic progenitor cell differentiation / methylated histone binding / kidney development / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / beta-catenin binding / transcription by RNA polymerase II / transcription coactivator activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fiedler, M. / Sanchez-Barrena, M.J. / Nekrasov, M. / Mieszczanek, J. / Rybin, V. / Muller, J. / Evans, P. / Bienz, M. | ||||||
![]() | ![]() Title: Decoding of Methylated Histone H3 Tail by the Pygo- Bcl9 Wnt Signaling Complex. Authors: Fiedler, M. / Sanchez-Barrena, M.J. / Nekrasov, M. / Mieszczanek, J. / Rybin, V. / Muller, J. / Evans, P. / Bienz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.1 KB | Display | ![]() |
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PDB format | ![]() | 22.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.2 KB | Display | ![]() |
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Full document | ![]() | 435.3 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vp7SC ![]() 2vpdC ![]() 2vpeC ![]() 2vpgC S: Starting model for refinement 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 on special symmetry positions |
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Components
#1: Protein | Mass: 6982.755 Da / Num. of mol.: 1 / Fragment: PHD DOMAIN, RESIDUES 333-397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 3758.405 Da / Num. of mol.: 1 / Fragment: HD1 DOMAIN, RESIDUES 174-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.32 % / Description: NONE |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING-DROP VAPOUR-DIFFUSION METHOD AT 19 CELSIUS. CRYSTALLIZATION CONDITIONS: 1M NA-CITRATE, 100MM TRIS PH7, 200MM NACL, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 16, 2007 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→28.56 Å / Num. obs: 15426 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 11.4 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VP7 Resolution: 1.59→60.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.301 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PYGO1 PHD RESIDUE S362 PRESENTS AN UNUSUAL CONFORMATION SINCE IT IS NEXT TO C363, WHICH IS PART OF THE ZN 2 BINDING SITE
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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: 22.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→60.08 Å
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Refine LS restraints |
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