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- PDB-3vh6: Crystal structure of the chicken CENP-T histone fold/CENP-W/CENP-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vh6 | ||||||
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Title | Crystal structure of the chicken CENP-T histone fold/CENP-W/CENP-S/CENP-X heterotetrameric complex, crystal form II | ||||||
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![]() | DNA BINDING PROTEIN / histone fold / chromosome segregation / DNA binding / nucleus | ||||||
Function / homology | ![]() PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / FANCM-MHF complex / Fanconi anaemia nuclear complex ...PKR-mediated signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Fanconi Anemia Pathway / FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / chromosome segregation / kinetochore / mitotic cell cycle / protein heterodimerization activity / cell division / DNA repair / chromatin binding / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nishino, T. / Takeuchi, K. / Gascoigne, K.E. / Suzuki, A. / Hori, T. / Oyama, T. / Morikawa, K. / Cheeseman, I.M. / Fukagawa, T. | ||||||
![]() | ![]() Title: CENP-T-W-S-X Forms a Unique Centromeric Chromatin Structure with a Histone-like Fold Authors: Nishino, T. / Takeuchi, K. / Gascoigne, K.E. / Suzuki, A. / Hori, T. / Oyama, T. / Morikawa, K. / Cheeseman, I.M. / Fukagawa, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.5 KB | Display | ![]() |
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PDB format | ![]() | 61.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.1 KB | Display | ![]() |
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Full document | ![]() | 469.1 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b0bC ![]() 3b0cC ![]() 3b0dC ![]() 3vh5SC 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: 15561.421 Da / Num. of mol.: 1 / Mutation: C26A, C28A, C55A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 9361.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 12682.790 Da / Num. of mol.: 1 / Fragment: C-terminal histone fold / Mutation: C87A, C161A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 8855.593 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
Sequence details | THE SEQUENCE DATABASE REFERENCES |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, 5.6% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2011 |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→37.4 Å / Num. all: 9985 / Num. obs: 9626 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 115.15 Å2 |
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.88 / Num. unique all: 938 / Rsym value: 0.726 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VH5 Resolution: 3.351→37.361 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7888 / SU ML: 1.09 / σ(F): 1.34 / Phase error: 27.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.058 Å2 / ksol: 0.326 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 352.23 Å2 / Biso mean: 117.7597 Å2 / Biso min: 59.68 Å2
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Refinement step | Cycle: LAST / Resolution: 3.351→37.361 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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