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Yorodumi- PDB-3uig: crystal structure of human Survivin in complex with T3 phosphoryl... -
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-Basic information
Entry | Database: PDB / ID: 3uig | ||||||
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Title | crystal structure of human Survivin in complex with T3 phosphorylated H3(1-15) peptide | ||||||
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Keywords | APOPTOSIS/APOPTOSIS INHIBITOR / BIR domain / mitosis / T3 phosphorylated H3 binding / Smac/Diablo binding / Phosphorylation / APOPTOSIS-APOPTOSIS INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / cobalt ion binding / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cytoplasmic microtubule / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / mitotic cytokinesis / chromosome, centromeric region / mitotic spindle assembly / telomere organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Chromatin modifying enzymes / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / centriole / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / tubulin binding / positive regulation of mitotic cell cycle / 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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / spindle microtubule / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / sensory perception of sound / 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 / kinetochore / G2/M transition of mitotic cell cycle / small GTPase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / structural constituent of chromatin / Separation of Sister Chromatids / microtubule cytoskeleton / 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 / mitotic cell cycle / Neddylation / HATs acetylate histones / protein-folding chaperone binding / gene expression / midbody / 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 / protein phosphorylation / cell division / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / 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: 2.4 Å | ||||||
Authors | Du, J. / Patel, D.J. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Structural Basis for Recognition of H3T3ph and Smac/DIABLO N-terminal Peptides by Human Survivin. Authors: Du, J. / Kelly, A.E. / Funabiki, H. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uig.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uig.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 3uig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uig_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
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Full document | 3uig_full_validation.pdf.gz | 477.8 KB | Display | |
Data in XML | 3uig_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3uig_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/3uig ftp://data.pdbj.org/pub/pdb/validation_reports/ui/3uig | HTTPS FTP |
-Related structure data
Related structure data | 3uihC 3uiiC 3uijC 3uikC 1f3hS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | the biological assembly is the same as the asymmetric unit. |
-Components
#1: Protein | Mass: 16471.787 Da / Num. of mol.: 2 / Fragment: unp residues 1-142 / Mutation: K139E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O15392 #2: Protein/peptide | Mass: 1645.777 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P68431*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: 3.64 Å3/Da / Density % sol: 66.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M DL-malic acid, pH 7.0, 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2010 |
Radiation | Monochromator: SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 20678 / Num. obs: 20244 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Rsym value: 0.527 / % possible all: 86.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F3H Resolution: 2.4→31.072 Å / SU ML: 0.44 / σ(F): 1.34 / σ(I): 0 / Phase error: 34.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.478 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→31.072 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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