+Open data
-Basic information
Entry | Database: PDB / ID: 2nqb | ||||||
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Title | Drosophila Nucleosome Structure | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / Nucleosome / NCP / chromatin / histone / STRUCTURAL PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / Factors involved in megakaryocyte development and platelet production ...HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RCAF complex / Factors involved in megakaryocyte development and platelet production / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / nuclear chromosome / nucleosomal DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / chromosome / nucleic acid binding / protein heterodimerization activity / protein-containing complex binding / chromatin / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Luger, K. / Chakravarthy, S. | ||||||
Citation | Journal: To be Published Title: Comparative analysis of nucleosome structures from different species. Authors: Chakravarthy, S. / Luger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nqb.cif.gz | 327.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nqb.ent.gz | 249.4 KB | Display | PDB format |
PDBx/mmJSON format | 2nqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nqb_validation.pdf.gz | 515 KB | Display | wwPDB validaton report |
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Full document | 2nqb_full_validation.pdf.gz | 551 KB | Display | |
Data in XML | 2nqb_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 2nqb_validation.cif.gz | 57.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/2nqb ftp://data.pdbj.org/pub/pdb/validation_reports/nq/2nqb | HTTPS FTP |
-Related structure data
Related structure data | 1aoiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Each nucleosome has two copies each of histones H2A, H2B, H3 and H4, and a 146 base pairs long palindromic strand of DNA derived from human alpha-satellite sequence. |
-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15289.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His4 / Production host: Escherichia coli (E. coli) / References: UniProt: P02299 #3: Protein | Mass: 11390.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2A / Production host: Escherichia coli (E. coli) / References: UniProt: P84040 #4: Protein | Mass: 13257.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: His2B / Production host: Escherichia coli (E. coli) / References: UniProt: P84051 #5: Protein | Mass: 13680.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P02283 |
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-DNA chain / Non-polymers , 2 types, 266 molecules IJ
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: His3 / Production host: Escherichia coli (E. coli) #6: 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: 2.64 Å3/Da / Density % sol: 53.37 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Constituents of the crystallization buffer: Potassium Chloride, Manganese Chloride, and Potassium Cacodylate., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. all: 94877 / Num. obs: 93949 / % possible obs: 98.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3 / Num. unique all: 5358 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AOI Resolution: 2.3→99 Å
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→99 Å
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Refine LS restraints |
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Xplor file |
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