+Open data
-Basic information
Entry | Database: PDB / ID: 4ouc | ||||||
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Title | Structure of human haspin in complex with histone H3 substrate | ||||||
Components |
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Keywords | TRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / histone / kinase substrate complex / Chromatin regulator | ||||||
Function / homology | Function and homology information histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein heterodimerization activity / Amyloid fiber formation / protein phosphorylation / protein serine kinase activity / centrosome / DNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol Cell Proteomics / Year: 2014 Title: Modulation of the chromatin phosphoproteome by the haspin protein kinase. Authors: Maiolica, A. / de Medina-Redondo, M. / Schoof, E.M. / Chaikuad, A. / Villa, F. / Gatti, M. / Jeganathan, S. / Lou, H.J. / Novy, K. / Hauri, S. / Toprak, U.H. / Herzog, F. / Meraldi, P. / ...Authors: Maiolica, A. / de Medina-Redondo, M. / Schoof, E.M. / Chaikuad, A. / Villa, F. / Gatti, M. / Jeganathan, S. / Lou, H.J. / Novy, K. / Hauri, S. / Toprak, U.H. / Herzog, F. / Meraldi, P. / Penengo, L. / Turk, B.E. / Knapp, S. / Linding, R. / Aebersold, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ouc.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ouc.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ouc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/4ouc ftp://data.pdbj.org/pub/pdb/validation_reports/ou/4ouc | HTTPS FTP |
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-Related structure data
Related structure data | 3iq7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN |
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 40711.484 Da / Num. of mol.: 1 / Fragment: UNP residues 465-798 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSG2 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-R3-pRARE2 References: UniProt: Q8TF76, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 1414.610 Da / Num. of mol.: 1 / Fragment: histone H3 tail, UNP residues 2-13 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3 |
-Non-polymers , 5 types, 428 molecules
#3: Chemical | ChemComp-NA / | ||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-5ID / ( | #6: Chemical | ChemComp-IOD / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.57 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.2M potassium thiocyanate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 23, 2012 |
Radiation | Monochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→33.59 Å / Num. all: 32592 / Num. obs: 32539 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4675 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3IQ7 Resolution: 1.9→31.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.185 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.134 / ESU R Free: 0.131 / 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: 25.618 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→31.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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