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- PDB-2f8n: 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes -

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Basic information

Entry
Database: PDB / ID: 2f8n
Title2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes
Components
  • Core histone macro-H2A.1
  • Histone 3, H2ba
  • Histone H2A type 1
  • Histone H2B.1
  • Histone H3.1
  • Histone H4
  • alpha-satellite DNA (146 bp)
KeywordsSTRUCTURAL PROTEIN/DNA / Nucleosome / NCP / macroH2A / Histone variant / chromatin / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


negative regulation of cell cycle G2/M phase transition / positive regulation of endodermal cell differentiation / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / Barr body / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / positive regulation of maintenance of mitotic sister chromatid cohesion / Interaction of NuRD complexes with transcription factors ...negative regulation of cell cycle G2/M phase transition / positive regulation of endodermal cell differentiation / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / Barr body / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / positive regulation of maintenance of mitotic sister chromatid cohesion / Interaction of NuRD complexes with transcription factors / DNA Damage/Telomere Stress Induced Senescence / regulation of response to oxidative stress / G2/M DNA damage checkpoint / Regulation of PD-L1(CD274) transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Negative Regulation of CDH1 Gene Transcription / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / PRC2 methylates histones and DNA / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Metalloprotease DUBs / UCH proteinases / Processing of DNA double-strand break ends / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / double-stranded methylated DNA binding / regulation of oxidative phosphorylation / RMTs methylate histone arginines / sex chromatin / Estrogen-dependent gene expression / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / rDNA binding / dosage compensation by inactivation of X chromosome / poly-ADP-D-ribose modification-dependent protein binding / Ub-specific processing proteases / establishment of protein localization to chromatin / positive regulation of keratinocyte differentiation / negative regulation of response to oxidative stress / negative regulation of gene expression, epigenetic / nuclear chromosome / regulation of lipid metabolic process / protein serine/threonine kinase inhibitor activity / pericentric heterochromatin / condensed chromosome / transcription initiation-coupled chromatin remodeling / site of DNA damage / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / epigenetic regulation of gene expression / chromatin DNA binding / nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / antibacterial humoral response / chromosome, telomeric region / transcription cis-regulatory region binding / chromosome / protein heterodimerization activity / DNA repair / nucleolus / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / : / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
Core histone macro-H2A / Core histone macro-H2A, macro domain / Histone, subunit A / Histone, subunit A / : / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B ...Core histone macro-H2A / Core histone macro-H2A, macro domain / Histone, subunit A / Histone, subunit A / : / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Core histone macro-H2A.1 / Histone H2B 1.1 / Histone H4 / Histone H3.2 / Histone H2A type 1-H / H2B.U histone 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChakravarthy, S. / Luger, K.
CitationJournal: To be Published
Title: Nucleosomes containing the histone domain of macroH2A: In vitro possibilities.
Authors: Chakravarthy, S. / Luger, K.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: alpha-satellite DNA (146 bp)
J: alpha-satellite DNA (146 bp)
A: Histone H3.1
B: Histone H4
D: Histone 3, H2ba
E: Histone H3.1
F: Histone H4
H: Histone H2B.1
G: Core histone macro-H2A.1
K: Histone H2A type 1


Theoretical massNumber of molelcules
Total (without water)200,60510
Polymers200,60510
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.145, 109.272, 176.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is an octamer of histones wrapped by 146 basepairs of DNA called the nucleosome core particle, which is also the asymmetric unit. (all of which, the coordinates are given for in the submitted pdb file).

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Components

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Protein , 6 types, 8 molecules AEBFDHGK

#2: Protein Histone H3.1


Mass: 15421.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: P84233
#3: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: P62799
#4: Protein Histone 3, H2ba


Mass: 14025.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: Q9D2U9
#5: Protein Histone H2B.1


Mass: 13655.948 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: P02281
#6: Protein Core histone macro-H2A.1


Mass: 12984.343 Da / Num. of mol.: 1 / Fragment: residues 0-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: O75367
#7: Protein Histone H2A type 1


Mass: 16198.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: Q8CGP6

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DNA chain / Non-polymers , 2 types, 122 molecules IJ

#1: DNA chain alpha-satellite DNA (146 bp)


Mass: 45054.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: puc19 / Production host: Escherichia coli (E. coli)
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MnCl211
3Potassium Cacodylate11
4H2O11
5KCl12
6MnCl212
7Potassium Cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→31.4 Å / Num. obs: 44768 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.07
Reflection shellHighest resolution: 2.9 Å / Rmerge(I) obs: 0.408

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1U35

1u35


Resolution: 2.9→31.4 Å / Stereochemistry target values: Engh & Huber
Details: A 73 chain I and T 74 chain I are linked together. A 217 chain J and T 218 chain J are linked together. However there are T 73A chain I and A 217A chain J present in the structure. The ...Details: A 73 chain I and T 74 chain I are linked together. A 217 chain J and T 218 chain J are linked together. However there are T 73A chain I and A 217A chain J present in the structure. The electron density for this base pair is lost as a result of a convolution between two stretch conformations on the two halves of the nucleosome on either side of the diad axis.
RfactorNum. reflectionSelection details
Rfree0.269 2184 Random
Rwork0.217 --
all-46170 -
obs-43333 -
Refinement stepCycle: LAST / Resolution: 2.9→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6007 5939 0 120 12066
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006598
X-RAY DIFFRACTIONc_angle_deg1.05529

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