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Yorodumi- PDB-4x8n: Crystal structure of Ash2L SPRY domain in complex with phosphoryl... -
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-Basic information
Entry | Database: PDB / ID: 4x8n | ||||||
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Title | Crystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5 | ||||||
Components |
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Keywords | PROTEIN BINDING / histone / MLL1 / chromatin / epigenetics | ||||||
Function / homology | Function and homology information MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / hemopoiesis / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / hemopoiesis / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / PKMTs methylate histone lysines / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / Neddylation / histone binding / transcription cis-regulatory region binding / DNA damage response / positive regulation of cell population proliferation / nucleolus / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Zhang, P. / Chaturvedi, C.P. / Brunzelle, J.S. / Skiniotis, G. / Brand, M. / Shilatifard, A. / Couture, J.-F. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Genes Dev. / Year: 2015 Title: A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation. Authors: Zhang, P. / Chaturvedi, C.P. / Tremblay, V. / Cramet, M. / Brunzelle, J.S. / Skiniotis, G. / Brand, M. / Shilatifard, A. / Couture, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x8n.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x8n.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 4x8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/4x8n ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x8n | 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
#1: Protein | Mass: 20322.094 Da / Num. of mol.: 1 / Fragment: UNP residues 380-495, 539-598 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASH2L, ASH2L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBL3 |
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#2: Protein/peptide | Mass: 1349.228 Da / Num. of mol.: 1 / Fragment: UNP residues 347-356 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15291 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.9 Å / Num. obs: 14095 / % possible obs: 98.6 % / Redundancy: 3.5 % / Net I/σ(I): 11.1 |
-Processing
Software |
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Refinement | Resolution: 2.1→29.9 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.48 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.234 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.9 Å
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Refine LS restraints |
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LS refinement shell |
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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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