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Yorodumi- PDB-3uef: Crystal structure of human Survivin bound to histone H3 (C2 space... -
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-Basic information
Entry | Database: PDB / ID: 3uef | ||||||
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Title | Crystal structure of human Survivin bound to histone H3 (C2 space group). | ||||||
Components |
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Keywords | CELL CYCLE / ZINC FINGER MOTIF / BIR DOMAIN / chromosomal passenger complex / cell division / mitosis | ||||||
Function / homology | Function and homology information survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization ...survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / protein-containing complex localization / chromosome passenger complex / cobalt ion binding / cysteine-type endopeptidase inhibitor activity / nuclear chromosome / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / mitotic cytokinesis / chromosome, centromeric region / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule / Chromatin modifying enzymes / epigenetic regulation of gene expression / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / telomere organization / centriole / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / positive regulation of mitotic cell cycle / tubulin binding / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / RHO GTPases Activate Formins / HDACs deacetylate histones / spindle microtubule / RNA Polymerase I Promoter Escape / sensory perception of sound / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / kinetochore / spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / small GTPase binding / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / nucleosome / mitotic cell cycle / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / gene expression / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / midbody / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / Oxidative Stress Induced Senescence / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / microtubule / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Niedzialkowska, E. / Porebski, P.J. / Wang, F. / Higgins, J.M. / Stukenberg, P.T. / Minor, W. | ||||||
Citation | Journal: Mol.Biol.Cell / Year: 2012 Title: Molecular basis for phosphospecific recognition of histone H3 tails by Survivin paralogues at inner centromeres. Authors: Niedzialkowska, E. / Wang, F. / Porebski, P.J. / Minor, W. / Higgins, J.M. / Stukenberg, P.T. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uef.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uef.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 3uef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/3uef ftp://data.pdbj.org/pub/pdb/validation_reports/ue/3uef | HTTPS FTP |
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-Related structure data
Related structure data | 3uecSC 3uedC 3ueeC 3uegC 3uehC 3ueiC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16826.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: API4, BIRC5, IAP4 / Plasmid: p8HIS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O15392 #2: Protein/peptide | Mass: 1308.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P68431*PLUS #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | E129K REPRESENTS | |
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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: 3.55 Å3/Da / Density % sol: 65.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 3350, 0.2 M potassium/sodium tartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: beryllium lens |
Radiation | Monochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 18747 / Num. obs: 18747 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / Num. unique all: 939 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UEC Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 13.047 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.192 / 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: 70.507 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.513 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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