+Open data
-Basic information
Entry | Database: PDB / ID: 4h9r | ||||||
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Title | Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/APOPTOSIS / histone chaperone / DNA BINDING PROTEIN-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 / regulation of protein ubiquitination / chromosome, centromeric region / spermatid development / extrinsic apoptotic signaling pathway via death domain receptors / subtelomeric heterochromatin formation / single fertilization / positive regulation of protein kinase activity / negative regulation of megakaryocyte differentiation / cellular response to unfolded protein / 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 / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / cellular response to copper ion / heat shock protein binding / 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 / Meiotic synapsis / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / SUMOylation of transcription cofactors / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / molecular condensate scaffold activity / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / multicellular organism growth / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PML body / DNA Damage/Telomere Stress Induced Senescence / 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 / structural constituent of chromatin / transcription corepressor activity / male gonad development / nucleosome / Regulation of TP53 Degradation / p53 binding / 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 / Processing of DNA double-strand break ends / cellular response to heat / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / regulation of gene expression / regulation of apoptotic process / Oxidative Stress Induced Senescence Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å | ||||||
Authors | Elsasser, S.J. / Huang, H. / Lewis, P.W. / Chin, J.W. / Allis, D.C. / Patel, D.J. | ||||||
Citation | Journal: To be Published Title: DAXX chaperone envelops an H3.3/H4 dimer dictating H3.3-specific read out Authors: Elsasser, S.J. / Huang, H. / Lewis, P.W. / Chin, J.W. / Allis, D.C. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h9r.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h9r.ent.gz | 138.9 KB | Display | PDB format |
PDBx/mmJSON format | 4h9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/4h9r ftp://data.pdbj.org/pub/pdb/validation_reports/h9/4h9r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15271.842 Da / Num. of mol.: 1 / Mutation: G90A, S96A, Y99F, G102A, A111T, M120F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243 | ||
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#2: Protein | Mass: 11263.231 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 Production host: Escherichia coli (E. coli) / References: UniProt: P62805 | ||
#3: Protein | Mass: 24667.293 Da / Num. of mol.: 1 / Fragment: UNP residues 178-389 / Mutation: E48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DAXX, BING2, DAP6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UER7 | ||
#4: Chemical | ChemComp-PO4 / #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: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.197→50 Å / Num. all: 27814 / Num. obs: 27814 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 33.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.197→38.968 Å / SU ML: 0.21 / σ(F): 1.36 / σ(I): 3.7 / Phase error: 23.87 / 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: 2.197→38.968 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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