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Yorodumi- PDB-3r93: Crystal structure of the chromo domain of M-phase phosphoprotein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r93 | ||||||
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Title | Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide | ||||||
Components |
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Keywords | CELL CYCLE / epigenetics / M-phase / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information positive regulation of DNA methylation-dependent heterochromatin formation / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / histone reader activity / heterochromatin / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / methylated histone binding ...positive regulation of DNA methylation-dependent heterochromatin formation / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / histone reader activity / heterochromatin / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / methylated histone binding / Interleukin-7 signaling / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / nucleolus / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.057 Å | ||||||
Authors | Li, J. / Li, Z. / Ruan, J. / Xu, C. / Tong, Y. / Pan, P.W. / Tempel, W. / Crombet, L. / Min, J. / Zang, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9. Authors: Li, J. / Li, Z. / Ruan, J. / Xu, C. / Tong, Y. / Pan, P.W. / Tempel, W. / Crombet, L. / Min, J. / Zang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r93.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r93.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 3r93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r93_validation.pdf.gz | 463.9 KB | Display | wwPDB validaton report |
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Full document | 3r93_full_validation.pdf.gz | 464 KB | Display | |
Data in XML | 3r93_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 3r93_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/3r93 ftp://data.pdbj.org/pub/pdb/validation_reports/r9/3r93 | HTTPS FTP |
-Related structure data
Related structure data | 3lweSC S: Starting model for refinement 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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Details | AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY INFORMATION FOR THE STRUCTURE IS UNKNOWN. |
-Components
#1: Protein | Mass: 7344.350 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q99549 #2: Protein/peptide | Mass: 1607.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: UniProt: Q71DI3*PLUS #3: Chemical | #4: 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: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 35% PEG2000-MME, 8-fold excess of H3K9Me3, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→50 Å / Num. obs: 24361 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.072 / Χ2: 1.824 / Net I/σ(I): 12.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3LWE Resolution: 2.057→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.486 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. The programs BUCCANEER, COOT were used as well as the MOLPROBITY server.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.11 Å2 / Biso mean: 40.273 Å2 / Biso min: 29.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.057→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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