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Yorodumi- PDB-1f3h: X-RAY CRYSTAL STRUCTURE OF THE HUMAN ANTI-APOPTOTIC PROTEIN SURVIVIN -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f3h | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF THE HUMAN ANTI-APOPTOTIC PROTEIN SURVIVIN | ||||||
Components | SURVIVIN | ||||||
Keywords | APOPTOSIS / APOPTOSIS INHIBITOR SURVIVIN / THIOL PROTEASE INHIBITOR / ALPHA-BETA | ||||||
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 / 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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / tubulin binding / positive regulation of mitotic cell cycle / RHO GTPases Activate Formins / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / spindle microtubule / kinetochore / small GTPase binding / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Neddylation / mitotic cell cycle / midbody / protein-folding chaperone binding / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / protein heterodimerization activity / 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 / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.58 Å | ||||||
Authors | Verdecia, M.A. / Huang, H. / Dutil, E. / Hunter, T. / Noel, J.P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Structure of the human anti-apoptotic protein survivin reveals a dimeric arrangement. Authors: Verdecia, M.A. / Huang, H. / Dutil, E. / Kaiser, D.A. / Hunter, T. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f3h.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f3h.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 1f3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f3h_validation.pdf.gz | 389.3 KB | Display | wwPDB validaton report |
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Full document | 1f3h_full_validation.pdf.gz | 408.7 KB | Display | |
Data in XML | 1f3h_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 1f3h_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f3h ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f3h | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16432.773 Da / Num. of mol.: 2 / Mutation: L54M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHIS8-3 / Production host: Escherichia coli (E. coli) / References: UniProt: O15392 #2: Chemical | #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: 3.9 Å3/Da / Density % sol: 68.47 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, LITHIUMSULPHATE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.58→54.12 Å / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 60.5 Å2 | ||||||||||||||||||||
Reflection shell | Resolution: 2.58→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.388 / % possible all: 95.5 | ||||||||||||||||||||
Reflection | *PLUS Num. obs: 15366 / % possible obs: 95.5 % / Num. measured all: 29469 / Rmerge(I) obs: 0.036 | ||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.349 |
-Processing
Software |
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Refinement | Resolution: 2.58→54.12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1711716.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.36 Å2 / ksol: 0.3262 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.58→54.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.58→2.74 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 83.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.448 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.406 |