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Open data
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Basic information
Entry | Database: PDB / ID: 4qlc | ||||||
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Title | Crystal structure of chromatosome at 3.5 angstrom resolution | ||||||
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![]() | CHROMATIN BINDING PROTEIN/DNA / NUCLEOSOME CORE PARTICLE / HISTONE FOLD / CHROMOSOME / CHROMATIN / Global histone H5 / gH5 / NCP167 / Regulation / SEGREGATION / CHROMATOSOME / gH1 / Liker Histone H5 / Linker DNA / Protein-DNA Complexes / DNA BINDING PROTEIN-DNA complex / CHROMATIN BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() HDMs demethylate histones / Interleukin-7 signaling / PKMTs methylate histone lysines / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins ...HDMs demethylate histones / Interleukin-7 signaling / PKMTs methylate histone lysines / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA Polymerase I Promoter Escape / polytene chromosome band / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / UCH proteinases / polytene chromosome / negative regulation of DNA recombination / chromosome condensation / nuclear chromosome / nucleosomal DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / chromosome / double-stranded DNA binding / nucleic acid binding / protein heterodimerization activity / protein-containing complex binding / chromatin / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, J.S. / Zhou, B.R. / Xiao, T.S. / Bai, Y.W. | ||||||
![]() | ![]() Title: Structural Mechanisms of Nucleosome Recognition by Linker Histones. Authors: Zhou, B.R. / Jiang, J. / Feng, H. / Ghirlando, R. / Xiao, T.S. / Bai, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 357.2 KB | Display | ![]() |
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PDB format | ![]() | 274.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1hstS ![]() 4inm S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
-DNA chain , 2 types, 2 molecules IJ
#1: DNA chain | Mass: 51325.676 Da / Num. of mol.: 1 / Fragment: 167bp Widom 601 DNA Source method: isolated from a genetically manipulated source Details: 147 BP WIDOM 601 DNA FRAGMENT and 20 bp linker DNA fragment Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 51783.977 Da / Num. of mol.: 1 / Fragment: 167bp Widom 601 DNA Source method: isolated from a genetically manipulated source Details: 147 BP WIDOM 601 DNA FRAGMENT and 20 bp linker DNA fragment Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 5 types, 9 molecules AEBFCGDHU
#3: Protein | Mass: 15289.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CG31613, CG33803, CG33806, CG33809, CG33812, CG33815, CG33818, CG33821, CG33824, CG33827, CG33830, CG33833, CG33836, CG33839, CG33842, CG33845, CG33848, CG33851, CG33854, CG33857, CG33860, ...Gene: CG31613, CG33803, CG33806, CG33809, CG33812, CG33815, CG33818, CG33821, CG33824, CG33827, CG33830, CG33833, CG33836, CG33839, CG33842, CG33845, CG33848, CG33851, CG33854, CG33857, CG33860, CG33863, CG33866, H3_DROME, His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866 Production host: ![]() ![]() #4: Protein | Mass: 11277.257 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first residue M is replaced by I / Source: (gene. exp.) ![]() ![]() Gene: CG31611, CG3379, CG33869, CG33871, CG33873, CG33875, CG33877, CG33879, CG33881, CG33883, CG33885, CG33887, CG33889, CG33891, CG33893, CG33895, CG33897, CG33899, CG33901, CG33903, CG33905, ...Gene: CG31611, CG3379, CG33869, CG33871, CG33873, CG33875, CG33877, CG33879, CG33881, CG33883, CG33885, CG33887, CG33889, CG33891, CG33893, CG33895, CG33897, CG33899, CG33901, CG33903, CG33905, CG33907, CG33909, H4, H4r, H4_DROME, His4, His4:CG31611, His4:CG33869, His4:CG33871, His4:CG33873, His4:CG33875, His4:CG33877, His4:CG33879, His4:CG33881, His4:CG33883, His4:CG33885, His4:CG33887, His4:CG33889, His4:CG33891, His4:CG33893, His4:CG33895, His4:CG33897, His4:CG33899, His4:CG33901, His4:CG33903, His4:CG33905, His4:CG33907, His4:CG33909, His4r Production host: ![]() ![]() #5: Protein | Mass: 13257.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: EKKA are replaced by DSHKAKAK / Source: (gene. exp.) ![]() ![]() Gene: CG31618, CG33808, CG33814, CG33817, CG33820, CG33823, CG33826, CG33829, CG33832, CG33835, CG33838, CG33841, CG33844, CG33847, CG33850, CG33862, CG33865, H2a, H2A_DROME, His2A, His2A:CG31618, ...Gene: CG31618, CG33808, CG33814, CG33817, CG33820, CG33823, CG33826, CG33829, CG33832, CG33835, CG33838, CG33841, CG33844, CG33847, CG33850, CG33862, CG33865, H2a, H2A_DROME, His2A, His2A:CG31618, His2A:CG33808, His2A:CG33814, His2A:CG33817, His2A:CG33820, His2A:CG33823, His2A:CG33826, His2A:CG33829, His2A:CG33832, His2A:CG33835, His2A:CG33838, His2A:CG33841, His2A:CG33844, His2A:CG33847, His2A:CG33850, His2A:CG33862, His2A:CG33865 Production host: ![]() ![]() #6: Protein | Mass: 13595.869 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first residue M is replaced by I / Source: (gene. exp.) ![]() ![]() Gene: CG17949, CG33868, CG33870, CG33872, CG33874, CG33876, CG33878, CG33880, CG33882, CG33884, CG33886, CG33888, CG33890, CG33892, CG33894, CG33896, CG33898, CG33900, CG33902, CG33904, CG33906, ...Gene: CG17949, CG33868, CG33870, CG33872, CG33874, CG33876, CG33878, CG33880, CG33882, CG33884, CG33886, CG33888, CG33890, CG33892, CG33894, CG33896, CG33898, CG33900, CG33902, CG33904, CG33906, CG33908, CG33910, H2B_DROME, His2B, His2B:CG17949, His2B:CG33868, His2B:CG33870, His2B:CG33872, His2B:CG33874, His2B:CG33876, His2B:CG33878, His2B:CG33880, His2B:CG33882, His2B:CG33884, His2B:CG33886, His2B:CG33888, His2B:CG33890, His2B:CG33892, His2B:CG33894, His2B:CG33896, His2B:CG33898, His2B:CG33900, His2B:CG33902, His2B:CG33904, His2B:CG33906, His2B:CG33908, His2B:CG33910 Production host: ![]() ![]() #7: Protein | | Mass: 8286.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HIS-tag at the N-term: MGSSHHHHHHSSGLVPRGSHMTE / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 1 types, 3 molecules ![](data/chem/img/CIT.gif)
#8: Chemical |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.75 Details: 0.1 mM Citric acid, 0.1mM potassium chloride, and 10% MPD, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 274 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→45.393 Å / Num. obs: 45664 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 91.5 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 1.3 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4INM, 1HST Resolution: 3.503→45.393 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.37 / Stereochemistry target values: TWIN_LSQ_F Details: Zero occupancy atoms represent atoms for which no electron density observed
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 137.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.503→45.393 Å
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Refine LS restraints |
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LS refinement shell |
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