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Yorodumi- PDB-2vp7: Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vp7 | ||||||
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Title | Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex | ||||||
Components |
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Keywords | GENE REGULATION / WNT SIGNALING PATHWAY / WNT SIGNALING COMPLEX / CHROMOSOMAL REARRANGEMENT / SIGNALING PROTEIN / PROTO-ONCOGENE / PHOSPHOPROTEIN / PYGO PHD DOMAIN / BCL9 HD1 DOMAIN / HISTONE H3K4ME2 TAIL / ZINC / NUCLEUS / ZINC-FINGER / METAL-BINDING | ||||||
Function / homology | Function and homology information 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Fiedler, M. / Sanchez-Barrena, M.J. / Nekrasov, M. / Mieszczanek, J. / Rybin, V. / Muller, J. / Evans, P. / Bienz, M. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vp7.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vp7.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/2vp7 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/2vp7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7661.530 Da / Num. of mol.: 1 / Fragment: PHD DOMAIN, RESIDUES 333-402 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS(DE3)-RIL / References: UniProt: Q9Y3Y4 | ||||||||
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#2: Protein/peptide | Mass: 3556.132 Da / Num. of mol.: 1 / Fragment: HD1 DOMAIN, RESIDUES 174-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS(DE3)-RIL / References: UniProt: O00512 | ||||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | MUTATION W366F | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.37 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: CRYSTALS WERE GROWN USING THE HANGING-DROP VAPOUR-DIFFUSION TECHNIQUE. CRYSTALLIZATION SOLUTION: 1.7M (NH4)2SO4, 100MM TRIS PH7.5, 200MM NACL, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 16, 2007 |
Radiation | Monochromator: SINGLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→24.96 Å / Num. obs: 12608 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.7 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.65→56.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.111 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ZN(II) NUMBER 2 AND ITS BINDING RESIDUES SHOW CERTAIN DISORDER
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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: 28.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→56.7 Å
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Refine LS restraints |
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