- PDB-2rvq: Solution structure of the isolated histone H2A-H2B heterodimer -
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Basic information
Entry
Database: PDB / ID: 2rvq
Title
Solution structure of the isolated histone H2A-H2B heterodimer
Components
Histone H2A type 1-B/E
Histone H2B type 1-J
Keywords
NUCLEAR PROTEIN/NUCLEAR PROTEIN / nucleosome / histone / H2A / H2B / DNA binding protein / CS-Rosetta / NUCLEAR PROTEIN-NUCLEAR PROTEIN complex
Function / homology
Function and homology information
negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / 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) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / 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 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / defense response to Gram-positive bacterium / Ub-specific processing proteases / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function
Method: CS-Rosetta-AbinitioRelax, CS-Rosetta-FloppyTail / Software ordinal: 1 Details: The structure of the core regions of H2A(Val27-Leu96) and H2B (Ser38-Lys125) connected by a random coil (Gly)16 poly-glycine linker was modeled by CS-Rosetta-AbinitioRelax protocol.In total ...Details: The structure of the core regions of H2A(Val27-Leu96) and H2B (Ser38-Lys125) connected by a random coil (Gly)16 poly-glycine linker was modeled by CS-Rosetta-AbinitioRelax protocol.In total 10,000 models were generated and selected the 10 models with the lowest CA-RMSD from the 20 models with the lowest CS-Rosetta energy., After the (Gly)16 poly-glycine linker was removed from each of the 10 selected structures of the H2A-H2B core, the flexible tails of H2A (Gly(-3)-Pro26 and Leu97-Lys129) and H2B (Gly(-3)-Tyr37) were connected by using MODELLER program. Next, for each of the three flexible tails,CS-Rosetta-FloppyTail protocol was used to generate 10,000 models for each of the 10 selected core structures, and selected one model with the lowest kai2 values of chemical shifts.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10000 / Conformers submitted total number: 10 / Representative conformer: 1
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