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- PDB-3av1: The human nucleosome structure containing the histone variant H3.2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3av1 | ||||||
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Title | The human nucleosome structure containing the histone variant H3.2 | ||||||
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Function / homology | ![]() negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome / Packaging Of Telomere Ends / Chromatin modifying enzymes / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / DNA replication-independent chromatin assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / Cleavage of the damaged pyrimidine ...negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome / Packaging Of Telomere Ends / Chromatin modifying enzymes / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / DNA replication-independent chromatin assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / SUMOylation of chromatin organization proteins / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tachiwana, H. / Osakabe, A. / Shiga, T. / Miya, Y. / Kimura, H. / Kagawa, W. / Kurumizaka, H. | ||||||
![]() | ![]() Title: Structures of human nucleosomes containing major histone H3 variants Authors: Tachiwana, H. / Osakabe, A. / Shiga, T. / Miya, Y. / Kimura, H. / Kagawa, W. / Kurumizaka, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 314.5 KB | Display | ![]() |
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PDB format | ![]() | 247 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.2 KB | Display | ![]() |
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Full document | ![]() | 427.6 KB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3av2C ![]() 3afaS 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
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15703.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 11676.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Protein | Mass: 14447.825 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Protein | Mass: 14217.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-DNA chain / Non-polymers , 2 types, 111 molecules IJ

#5: DNA chain | Mass: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The DNA sequence is palindromic, containing two halves a human alpha-satellite repeat. #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.15 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 74344 / Num. obs: 74215 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 60.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3AFA Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell |
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