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- PDB-1u35: Crystal structure of the nucleosome core particle containing the ... -

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Basic information

Entry
Database: PDB / ID: 1u35
TitleCrystal structure of the nucleosome core particle containing the histone domain of macroH2A
Components
  • H2A histone family
  • Hist1h4i protein
  • Histone H3.1Histone H3
  • alpha-satellite DNA
  • histone 3, H2ba
Keywordsstructural protein/DNA / Nucleosome / NCP / Histone fold / Histone variant / macroH2A / structural protein-DNA COMPLEX
Function / homology
Function and homology information


nucleosome => GO:0000786 / Inhibition of DNA recombination at telomere / chromatin organization => GO:0006325 / negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / HDACs deacetylate histones / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / negative regulation of response to oxidative stress ...nucleosome => GO:0000786 / Inhibition of DNA recombination at telomere / chromatin organization => GO:0006325 / negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / HDACs deacetylate histones / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / negative regulation of response to oxidative stress / DNA Damage/Telomere Stress Induced Senescence / regulation of response to oxidative stress / Barr body / Recognition and association of DNA glycosylase with site containing an affected purine / ADP-D-ribose binding / Chromatin modifying enzymes / SUMOylation of chromatin organization proteins / Deposition of new CENPA-containing nucleosomes at the centromere / Cleavage of the damaged purine / Condensation of Prophase Chromosomes / Interleukin-7 signaling / G2/M DNA damage checkpoint / HDMs demethylate histones / Processing of DNA double-strand break ends / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / Nonhomologous End-Joining (NHEJ) / sex-chromosome dosage compensation / sex chromatin / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / establishment of protein localization to chromatin / positive regulation of endodermal cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / double-stranded methylated DNA binding / rDNA binding / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / DNA replication-dependent chromatin assembly / regulation of oxidative phosphorylation / negative regulation of protein serine/threonine kinase activity / protein serine/threonine kinase inhibitor activity / positive regulation of keratinocyte differentiation / poly-ADP-D-ribose modification-dependent protein binding / nucleosomal DNA binding / negative regulation of gene expression, epigenetic / nuclear chromosome / site of DNA damage / regulation of lipid metabolic process / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / CENP-A containing nucleosome / epigenetic regulation of gene expression / condensed chromosome / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / DNA-templated transcription initiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / chromosome, telomeric region / transcription cis-regulatory region binding / protein heterodimerization activity / protein domain specific binding / DNA repair / chromatin / nucleolus / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Core histone macro-H2A / Core histone macro-H2A, macro domain / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Core histone macro-H2A / Core histone macro-H2A, macro domain / Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Core histone macro-H2A.1 / Histone H4 / Histone H3.1 / Histone H4 / H2B.U histone 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChakravarthy, S. / Gundimella, S.K. / Caron, C. / Perche, P.Y. / Pehrson, J.R. / Khochbin, S. / Luger, K.
CitationJournal: Mol.Cell.Biol. / Year: 2005
Title: Structural characterization of the histone variant macroH2A.
Authors: Chakravarthy, S. / Gundimella, S.K. / Caron, C. / Perche, P.Y. / Pehrson, J.R. / Khochbin, S. / Luger, K.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: alpha-satellite DNA
J: alpha-satellite DNA
A: Histone H3.1
B: Hist1h4i protein
C: H2A histone family
D: histone 3, H2ba
E: Histone H3.1
F: Hist1h4i protein
G: H2A histone family
H: histone 3, H2ba


Theoretical massNumber of molelcules
Total (without water)197,79210
Polymers197,79210
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.505, 109.598, 175.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3.1 / Histone H3 / H3/a / H3/c / H3/d / H3/f / H3/h / H3/i / H3/j / H3/k / H3/l


Mass: 15437.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H3FA, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL / Plasmid: pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLysS / References: UniProt: P68433
#3: Protein Hist1h4i protein / member Y isoform 1 / histone macroH2A1.2 / histone macroH2A1.1


Mass: 11394.426 Da / Num. of mol.: 2
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: Q5T006, UniProt: P62806*PLUS
#4: Protein H2A histone family


Mass: 12984.343 Da / Num. of mol.: 2
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
#5: Protein histone 3, H2ba /


Mass: 14025.280 Da / Num. of mol.: 2
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

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DNA chain / Non-polymers , 2 types, 107 molecules IJ

#1: DNA chain alpha-satellite DNA


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) / Strain (production host): DH5-alpha
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: potassium chloride, manganese chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1potassium chloride11
2manganese chloride11
3potassium cacodylate11
4H2O11
5potassium chloride12
6manganese chloride12
7potassium cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 43366 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.95→3.02 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.15 / Num. unique all: 2865 / % possible all: 100

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Processing

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

1aoi


Resolution: 3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: There are close contacts between A217 and T218 in chain J, between T74 and C75 in chain I.
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 2004 -random
Rwork0.206 ---
all-41583 --
obs-39783 95.7 %-
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6009 5939 0 105 12053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBonds0.0068
X-RAY DIFFRACTIONAngles1.0924

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