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Yorodumi- PDB-4llb: Crystal Structure of MOZ double PHD finger histone H3K14ac complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4llb | ||||||
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Title | Crystal Structure of MOZ double PHD finger histone H3K14ac complex | ||||||
Components |
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Keywords | TRANSFERASE / DPF - H3K14ac complex / zinc finger / plant homeodomain / double PHD finger / DPF / histone acetyltransferase / histone H3 tail | ||||||
Function / homology | Function and homology information histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / protein acetylation ...histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / protein acetylation / acetyltransferase activity / chromosome organization / Chromatin modifying enzymes / histone acetyltransferase activity / epigenetic regulation of gene expression / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / 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 signal transduction by p53 class mediator / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / transcription coregulator activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PML body / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / nucleosome / cellular senescence / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / nucleolus / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Dreveny, I. / Deeves, S.E. / Yue, B. / Heery, D.M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: The double PHD finger domain of MOZ/MYST3 induces alpha-helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification. Authors: Dreveny, I. / Deeves, S.E. / Fulton, J. / Yue, B. / Messmer, M. / Bhattacharya, A. / Collins, H.M. / Heery, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4llb.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4llb.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4llb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/4llb ftp://data.pdbj.org/pub/pdb/validation_reports/ll/4llb | HTTPS FTP |
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-Related structure data
Related structure data | 4ljnSC 4lk9C 4lkaC C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: chain D and segid) NCS domain segments: (Selection details: chain 'D' and segid ' ') |
-Components
#1: Protein | Mass: 15499.267 Da / Num. of mol.: 2 / Fragment: unp residues 194-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KAT6A, MOZ, MYST3, RUNXBP2, ZNF220 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q92794, histone acetyltransferase #2: Protein/peptide | Mass: 2302.679 Da / Num. of mol.: 2 / Fragment: unp residues 2-22 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431 #3: Chemical | ChemComp-ZN / #4: 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: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion / pH: 8.5 Details: 100 mM Tris-Cl, 200 mM Li2SO4, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91732 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 3, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91732 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→29.1 Å / Num. all: 11753 / Num. obs: 11753 / % possible obs: 99.6 % / Redundancy: 9.5 % / Biso Wilson estimate: 27.97 Å2 / Rsym value: 0.157 / Net I/σ(I): 12.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4LJN Resolution: 2.5→29.1 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8127 / SU ML: 0.3 / σ(F): 0 / Phase error: 25.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.32 Å2 / Biso mean: 34.8729 Å2 / Biso min: 10.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.1 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 102 / Type: POSITIONAL / Rms dev position: 0.131 Å | ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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