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- PDB-2rvq: Solution structure of the isolated histone H2A-H2B heterodimer -

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Basic information

Entry
Database: PDB / ID: 2rvq
TitleSolution structure of the isolated histone H2A-H2B heterodimer
Components
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
KeywordsNUCLEAR 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 / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / 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 / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / Ub-specific processing proteases / defense response to Gram-positive bacterium / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / CS-Rosetta-AbinitioRelax, CS-Rosetta-FloppyTail
Model detailslowest energy, model1
AuthorsMoriwaki, Y. / Yamane, T. / Ohtomo, H. / Ikeguchi, M. / Kurita, J. / Sato, M. / Nagadoi, A. / Shimojo, H. / Nishimura, Y.
CitationJournal: Sci Rep / Year: 2016
Title: Solution structure of the isolated histone H2A-H2B heterodimer
Authors: Moriwaki, Y. / Yamane, T. / Ohtomo, H. / Ikeguchi, M. / Kurita, J. / Sato, M. / Nagadoi, A. / Shimojo, H. / Nishimura, Y.
History
DepositionMar 28, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J


Theoretical massNumber of molelcules
Total (without water)28,5232
Polymers28,5232
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14376.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#2: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14146.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TROSY-HN(CO)CACB
121TROSY-HN(CA)CB
131TROSY-HN(CA)CO
141TROSY-HNCO
151(H)CC(CO)NH
161TROSY-1H-15N HSQC
171TROSY-1H-13C HSQC

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Sample preparation

DetailsContents: 0.1-0.3 mM [U-13C; U-15N; U-2H] entity_1-1, 0.1-0.3 mM [U-13C; U-15N; U-2H] entity_2-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-13C; U-15N; U-2H]0.1-0.31
mMentity_2-2[U-13C; U-15N; U-2H]0.1-0.31
Sample conditionsIonic strength: 400 / pH: 6.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance8002

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Processing

NMR software
NameDeveloperClassification
CS-RosettaShen, Vernon, Baker and Baxgeometry optimization
CS-RosettaShen, Vernon, Baker and Baxrefinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 10 / Representative conformer: 1

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