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- PDB-3uee: Crystal structure of human Survivin K62A mutant bound to N-termin... -
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Basic information
Entry | Database: PDB / ID: 3uee | ||||||
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Title | Crystal structure of human Survivin K62A mutant bound to N-terminal histone H3 | ||||||
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![]() | CELL CYCLE / ZINC FINGER MOTIF / BIR DOMAIN / chromosomal passenger complex / cell division / mitosis | ||||||
Function / homology | ![]() survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / 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 mitotic cytokinesis / positive regulation of exit from mitosis / 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 / 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 / cobalt ion binding / cytoplasmic microtubule / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic cytokinesis / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 / tubulin binding / positive regulation of mitotic cell cycle / 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 / RHO GTPases Activate Formins / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / sensory perception of sound / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / spindle microtubule / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / kinetochore / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / small GTPase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / midbody / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / microtubule / Estrogen-dependent gene expression / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niedzialkowska, E. / Porebski, P.J. / Wang, F. / Higgins, J.M. / Stukenberg, P.T. / Minor, W. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.3 KB | Display | ![]() |
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PDB format | ![]() | 100 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 434.8 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3uecSC ![]() 3uedC ![]() 3uefC ![]() 3uegC ![]() 3uehC ![]() 3ueiC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16768.025 Da / Num. of mol.: 2 / Mutation: K62A, E129K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1308.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P68431*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | E129K REPRESENTS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG 3350, 0.12 M succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.6→50 Å / Num. all: 15257 / Num. obs: 15257 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 82.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 38.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / Num. unique all: 704 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UEC Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 17.584 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.251 / 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: 80.333 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.612→2.68 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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