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- PDB-6a7u: Crystal structure of histone H2A.Bbd-H2B dimer -

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Basic information

Entry
Database: PDB / ID: 6a7u
TitleCrystal structure of histone H2A.Bbd-H2B dimer
ComponentsHistone H2B type 2-E,Histone H2A-Bbd type 2/3
KeywordsDNA BINDING PROTEIN / Histone / Histone variant / H2A.Bbd
Function / homology
Function and homology information


Replacement of protamines by nucleosomes in the male pronucleus / 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 ...Replacement of protamines by nucleosomes in the male pronucleus / 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) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / 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 / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / mRNA processing / 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 / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Ub-specific processing proteases / defense response to Gram-positive bacterium / Amyloid fiber formation / protein heterodimerization activity / 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 / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / 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-Bbd type 2/3 / Histone H2B type 2-E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDai, L. / Zhou, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of the histone heterodimer containing histone variant H2A.Bbd.
Authors: Dai, L. / Xie, X. / Zhou, Z.
History
DepositionJul 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H2B type 2-E,Histone H2A-Bbd type 2/3


Theoretical massNumber of molelcules
Total (without water)26,5341
Polymers26,5341
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.640, 141.910, 56.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histone H2B type 2-E,Histone H2A-Bbd type 2/3 / Histone H2B-GL105 / Histone H2B.q / H2B/q / H2A Barr body-deficient / H2A.Bbd


Mass: 26534.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST2H2BE, H2BFQ, H2AFB2, H2AFB3, H2ABBD, H2AFB / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q16778, UniProt: P0C5Z0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium citrate tribasic dihydrate pH5.5 38% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.6→44.39 Å / Num. obs: 8011 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.7
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.696 / Num. unique obs: 959 / CC1/2: 0.901

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFA

3afa


Resolution: 2.6→44.39 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.52
RfactorNum. reflection% reflection
Rfree0.2629 457 5.73 %
Rwork0.235 --
obs0.2367 7979 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 0 4 1330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011344
X-RAY DIFFRACTIONf_angle_d1.4291816
X-RAY DIFFRACTIONf_dihedral_angle_d8.137825
X-RAY DIFFRACTIONf_chiral_restr0.058217
X-RAY DIFFRACTIONf_plane_restr0.006229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.97630.28521490.30162457X-RAY DIFFRACTION100
2.9763-3.74960.24881450.24422475X-RAY DIFFRACTION100
3.7496-44.40110.26411630.2162590X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.753 Å / Origin y: -25.7058 Å / Origin z: 3.0432 Å
111213212223313233
T0.3299 Å20.009 Å20.0406 Å2-0.322 Å20.0015 Å2--0.3252 Å2
L0.9031 °2-0.4298 °2-0.7958 °2-0.5382 °2-0.0796 °2--0.7696 °2
S0.22 Å °-0.0843 Å °0.0498 Å °-0.011 Å °0.075 Å °-0.0327 Å °-0.0431 Å °-0.0855 Å °0 Å °
Refinement TLS groupSelection details: all

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