+Open data
-Basic information
Entry | Database: PDB / ID: 4h9s | ||||||
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Title | Complex structure 6 of DAXX/H3.3(sub7)/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 / cellular response to cadmium ion / Replacement of protamines by nucleosomes in the male pronucleus / single fertilization / positive regulation of protein kinase activity / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to unfolded protein / lipoxygenase pathway / telomere organization / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / JNK cascade / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / cellular response to copper ion / heat shock protein binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / embryo implantation / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / SUMOylation of transcription cofactors / molecular condensate scaffold activity / Defective pyroptosis / Meiotic recombination / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / 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 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / PML body / p53 binding / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Regulation of TP53 Degradation / osteoblast differentiation / structural constituent of chromatin / transcription corepressor activity / male gonad development / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / positive regulation of cell growth / histone binding / cellular response to heat / chromosome, telomeric region / Oxidative Stress Induced Senescence / regulation of apoptotic process / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / chromatin remodeling / nuclear body / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / nucleolus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 4h9s.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h9s.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 4h9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h9s_validation.pdf.gz | 479.8 KB | Display | wwPDB validaton report |
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Full document | 4h9s_full_validation.pdf.gz | 485.3 KB | Display | |
Data in XML | 4h9s_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 4h9s_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/4h9s ftp://data.pdbj.org/pub/pdb/validation_reports/h9/4h9s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15328.918 Da / Num. of mol.: 2 / Mutation: A75C, F84W, 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 #2: Protein | Mass: 9409.056 Da / Num. of mol.: 2 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: 25326.129 Da / Num. of mol.: 2 / Fragment: UNP residues 178-389 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 / | |
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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: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 30321 / Num. obs: 30321 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 36.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.092 Å / SU ML: 0.75 / σ(F): 1.33 / σ(I): 4.8 / Phase error: 25.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.355 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→44.092 Å
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Refine LS restraints |
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LS refinement shell |
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