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- PDB-3azg: Crystal Structure of Human Nucleosome Core Particle Containing H3... -

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Basic information

Entry
Database: PDB / ID: 3azg
TitleCrystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation
Components
  • 146-MER DNA
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1Histone H3
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / HISTONE-FOLD / NUCLEOSOME / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome / Packaging Of Telomere Ends / Chromatin modifying enzymes / regulation of gene expression, epigenetic / 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 / DNA replication-independent chromatin assembly / negative regulation of tumor necrosis factor-mediated signaling pathway ...negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome / Packaging Of Telomere Ends / Chromatin modifying enzymes / regulation of gene expression, epigenetic / 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 / DNA replication-independent chromatin assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / SUMOylation of chromatin organization proteins / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / DNA methylation / HCMV Late Events / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / heterochromatin assembly / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / lipopolysaccharide binding / Metalloprotease DUBs / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / RMTs methylate histone arginines / nucleosome assembly / HDMs demethylate histones / HCMV Early Events / Pre-NOTCH Transcription and Translation / Meiotic recombination / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosome / UCH proteinases / DNA-templated transcription, initiation / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / killing of cells of another organism / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / chromosome, telomeric region / antimicrobial humoral immune response mediated by antimicrobial peptide / Ub-specific processing proteases / cadherin binding / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein domain specific binding / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / 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. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A / Histone H2A / 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 / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2B type 1-J / Histone H4 / Histone H2A type 1-B/E / : / DNA (> 100) / DNA (> 10) / DNA / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsIwasaki, W. / Tachiwana, H. / Kawaguchi, K. / Shibata, T. / Kagawa, W. / Kurumizaka, H.
CitationJournal: Biochemistry / Year: 2011
Title: Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains
Authors: Iwasaki, W. / Tachiwana, H. / Kawaguchi, K. / Shibata, T. / Kagawa, W. / Kurumizaka, H.
History
DepositionMay 25, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: 146-MER DNA
J: 146-MER DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,86523
Polymers202,22910
Non-polymers63613
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56150 Å2
ΔGint-411 kcal/mol
Surface area71570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.527, 109.772, 182.365
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

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


Mass: 15718.393 Da / Num. of mol.: 2 / Mutation: K115Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68431
#2: Protein Histone H4 /


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06899

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DNA chain , 1 types, 2 molecules IJ

#5: DNA chain 146-MER DNA


Mass: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 116 molecules

#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2009
RadiationMonochromator: Double-crystal monochromator, Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 84116 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 56.1 Å2 / Rsym value: 0.085
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8254 / Rsym value: 0.768 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CV5

2cv5


Resolution: 2.4→39.16 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4196 5 %RANDOM
Rwork0.226 ---
obs-84030 99.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6010 5939 13 103 12065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 2.4→2.48 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.358 417 -
Rwork0.307 7714 -
obs-8131 97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5cis_peptide.param

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