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Yorodumi- PDB-4hga: Structure of the variant histone H3.3-H4 heterodimer in complex w... -
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-Basic information
Entry | Database: PDB / ID: 4hga | ||||||
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Title | Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX | ||||||
Components |
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Keywords | CHAPERONE/APOPTOSIS / histone chaperone / CHAPERONE-APOPTOSIS complex | ||||||
Function / homology | Function and homology information cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation ...cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / transcription regulator inhibitor activity / oocyte maturation / nuclear androgen receptor binding / nucleus organization / protein kinase activator activity / androgen receptor signaling pathway / spermatid development / regulation of protein ubiquitination / chromosome, centromeric region / extrinsic apoptotic signaling pathway via death domain receptors / cellular response to unfolded protein / single fertilization / subtelomeric heterochromatin formation / positive regulation of protein kinase activity / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / JNK cascade / heat shock protein binding / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / cellular response to copper ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / cellular response to cadmium ion / telomere organization / embryo implantation / Meiotic synapsis / RNA Polymerase I Promoter Opening / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of transcription cofactors / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PML body / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / osteoblast differentiation / Transcriptional regulation of granulopoiesis / male gonad development / structural constituent of chromatin / transcription corepressor activity / nucleosome / p53 binding / Regulation of TP53 Degradation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / cellular response to heat / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.799 Å | ||||||
Authors | Liu, C.P. / Xiong, C.Y. / Wang, M.Z. / Yu, Z.L. / Yang, N. / Chen, P. / Zhang, Z.G. / Li, G.H. / Xu, R.M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX. Authors: Liu, C.P. / Xiong, C.Y. / Wang, M.Z. / Yu, Z.L. / Yang, N. / Chen, P. / Zhang, Z.G. / Li, G.H. / Xu, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hga.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hga.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 4hga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hga_validation.pdf.gz | 677.8 KB | Display | wwPDB validaton report |
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Full document | 4hga_full_validation.pdf.gz | 683 KB | Display | |
Data in XML | 4hga_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 4hga_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/4hga ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hga | 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: 24805.361 Da / Num. of mol.: 1 / Fragment: HISTONE BINDING DOMAIN, UNP RESIDUES 184-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DAXX, BING2, DAP6 / Plasmid: PGEX-6P-Xu / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: Q9UER7 | ||
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#2: Protein | Mass: 15360.983 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: P84243 | ||
#3: Protein | Mass: 11394.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: P62805 | ||
#4: Chemical | ChemComp-PC4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.1M HEPES-Na, pH 7.6, 23% (v/v) PEG 3350, 0.25M Ammonium acetate, 1% Tacsimate pH 7.0, 6% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.07 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.799→50 Å / Num. all: 13301 / Num. obs: 13274 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 1.91 / Num. unique all: 1254 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.799→44.934 Å / SU ML: 0.34 / σ(F): 1.36 / Phase error: 24.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.799→44.934 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: 5
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Refinement TLS params. | Method: refined / Origin x: 39.1942 Å / Origin y: 22.8178 Å / Origin z: 150.9987 Å
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Refinement TLS group | Selection details: ALL |