[English] 日本語

- PDB-1o9s: Crystal structure of a ternary complex of the human histone methy... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1o9s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a ternary complex of the human histone methyltransferase SET7/9 | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / METHYLATION / HISTONE H3 / METHYLTRANSFERASE | ||||||
Function / homology | ![]() heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / regulation of DNA repair / Chromatin modifying enzymes ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / regulation of DNA repair / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / 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 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / 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 / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / p53 binding / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / response to ethanol / Estrogen-dependent gene expression / gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / chromatin binding / positive regulation of DNA-templated transcription / nucleolus / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xiao, B. / Jing, C. / Wilson, J.R. / Walker, P.A. / Vasisht, N. / Kelly, G. / Howell, S. / Taylor, I.A. / Blackburn, G.M. / Gamblin, S.J. | ||||||
![]() | ![]() Title: Structure and Catalytic Mechanism of the Human Histone Methyltransferase Set7/9 Authors: Xiao, B. / Jing, C. / Wilson, J.R. / Walker, P.A. / Vasisht, N. / Kelly, G. / Howell, S. / Taylor, I.A. / Blackburn, G.M. / Gamblin, S.J. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 228 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 179.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 514.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 526.5 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h3iS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | THE DIMER IN THIS ENTRY IS FORMED BY THE COMPLEXOF CHAIN A WITH A PEPTIDE CHAIN K AND CHAIN B WITHPEPTIDE CHAIN L. CHAINS A AND B ARE MONOMERIC IN THEPHYSIOLOGICAL STATE. |
-
Components
#1: Protein | Mass: 28912.133 Da / Num. of mol.: 2 / Fragment: N-DOMAIN, SET-DOMAIN, RESIDUES 108-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8WTS6, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1239.447 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-11 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.85 % |
---|---|
Crystal grow | pH: 7.8 / Details: pH 7.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 54703 / % possible obs: 89.9 % / Redundancy: 22 % / Rsym value: 0.055 / Net I/σ(I): 47.2 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H3I Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
|