[English] 日本語
Yorodumi- PDB-4ft2: crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ft2 | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 peptide and SAH | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / chromodomain / BAH domain / DNA methyltransferase domain / DNA methyltransferase / H3K9me2 binding / methylation | ||||||
Function / homology | Function and homology information DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / negative regulation of gene expression via chromosomal CpG island methylation / telomere organization / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation ...DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / negative regulation of gene expression via chromosomal CpG island methylation / telomere organization / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / 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 / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / 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 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / Oxidative Stress Induced Senescence / methylation / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Du, J. / Patel, D.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2012 Title: Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants. Authors: Du, J. / Zhong, X. / Bernatavichute, Y.V. / Stroud, H. / Feng, S. / Caro, E. / Vashisht, A.A. / Terragni, J. / Chin, H.G. / Tu, A. / Hetzel, J. / Wohlschlegel, J.A. / Pradhan, S. / Patel, D.J. / Jacobsen, S.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ft2.cif.gz | 551.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ft2.ent.gz | 453.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ft2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ft2_validation.pdf.gz | 962.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ft2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ft2_validation.xml.gz | 67.8 KB | Display | |
Data in CIF | 4ft2_validation.cif.gz | 90 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/4ft2 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/4ft2 | HTTPS FTP |
-Related structure data
Related structure data | 4fsxSC 4ft4C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 87591.828 Da / Num. of mol.: 2 / Fragment: UNP residues 130-912 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: MET2A, ZMET2 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL References: UniProt: Q9AXT8, DNA (cytosine-5-)-methyltransferase #2: Protein/peptide | | Mass: 1592.843 Da / Num. of mol.: 1 / Fragment: histone H3 peptide, UNP residues 16-30 / Source method: obtained synthetically / Details: H3 peptide was synthesized / References: UniProt: P68431 #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.12 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M calcium acetate, 0.1 M imidazole pH 8.0, and 10% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 39197 / Num. obs: 38805 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.503 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FSX Resolution: 3.2→40.099 Å / SU ML: 1.04 / σ(F): 1.98 / Phase error: 28.7 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.828 Å2 / ksol: 0.281 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→40.099 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|