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- PDB-5gxq: The crystal structure of the nucleosome containing H3.6 -

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Basic information

Entry
Database: PDB / ID: 5gxq
TitleThe crystal structure of the nucleosome containing H3.6
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.6
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / Chromatin / Nucleosome / Histone variant / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / 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 ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / 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 / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / 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 / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / 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 / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsTaguchi, H. / Xie, Y. / Horikoshi, N. / Kurumizaka, H.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25116002 Japan
Japan Society for the Promotion of ScienceJP25250023 Japan
Japan Agency for Medical Research and Development (AMED) Japan
Japan Society for the Promotion of Science16J09361 Japan
CitationJournal: Biochemistry / Year: 2017
Title: Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8
Authors: Taguchi, H. / Xie, Y. / Horikoshi, N. / Maehara, K. / Harada, A. / Nogami, J. / Sato, K. / Arimura, Y. / Osakabe, A. / Kujirai, T. / Iwasaki, T. / Semba, Y. / Tachibana, T. / Kimura, H. / ...Authors: Taguchi, H. / Xie, Y. / Horikoshi, N. / Maehara, K. / Harada, A. / Nogami, J. / Sato, K. / Arimura, Y. / Osakabe, A. / Kujirai, T. / Iwasaki, T. / Semba, Y. / Tachibana, T. / Kimura, H. / Ohkawa, Y. / Kurumizaka, H.
History
DepositionSep 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Histone H3.6
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.6
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)201,87210
Polymers201,87210
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56100 Å2
ΔGint-401 kcal/mol
Surface area73210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.026, 109.764, 181.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone H3.6


Mass: 15540.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3AP6 / Plasmid: pH3.6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1X8XL64*PLUS
#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) / Gene: HIST1H4A / Plasmid: pH4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB / Plasmid: pH2A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ / Plasmid: pH2B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06899
#5: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEM-T(Easy) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha
Sequence detailsUniProt database of chain A, E does not currently exist, but Nucleotide database code is NG_022939. ...UniProt database of chain A, E does not currently exist, but Nucleotide database code is NG_022939.1 in GenBank. Three N-terminal residues, GSH are expression tags.

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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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 50454 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 59.82 Å2 / Rmerge(I) obs: 0.084 / Χ2: 2.601 / Net I/av σ(I): 34.717 / Net I/σ(I): 13.5 / Num. measured all: 297098
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.85-2.955.90.4641100
2.95-3.075.90.3631100
3.07-3.215.90.2621100
3.21-3.3860.1731100
3.38-3.5960.1281100
3.59-3.8760.0941100
3.87-4.2660.071100
4.26-4.8760.0561100
4.87-6.145.90.0541100
6.14-505.40.048196.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.84 Å40.64 Å
Translation2.84 Å40.64 Å

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Processing

Software
NameVersionClassification
HKL-20000.98.704kdata scaling
PHASER2.1.4phasing
PDB_EXTRACT3.2data extraction
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFA

3afa


Resolution: 2.85→38.129 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2618 2534 5.07 %
Rwork0.2191 47450 -
obs0.2213 49984 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.05 Å2 / Biso mean: 70.4353 Å2 / Biso min: 19.5 Å2
Refinement stepCycle: final / Resolution: 2.85→38.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6001 5980 0 0 11981
Num. residues----1050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112791
X-RAY DIFFRACTIONf_angle_d1.14718527
X-RAY DIFFRACTIONf_chiral_restr0.0542104
X-RAY DIFFRACTIONf_plane_restr0.0061336
X-RAY DIFFRACTIONf_dihedral_angle_d26.1116678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.90480.35261520.285626072759100
2.9048-2.96410.38081320.282726352767100
2.9641-3.02850.32451580.258125952753100
3.0285-3.09890.27511320.247725932725100
3.0989-3.17640.29341610.240426002761100
3.1764-3.26220.2361340.252126162750100
3.2622-3.35810.30191170.249626272744100
3.3581-3.46650.28661300.228126272757100
3.4665-3.59030.26461590.218226002759100
3.5903-3.73390.27371300.214626372767100
3.7339-3.90370.31420.215126552797100
3.9037-4.10930.25261480.207226292777100
4.1093-4.36640.22831310.199126382769100
4.3664-4.7030.24121360.201826422778100
4.703-5.17520.25881620.201826662828100
5.1752-5.92170.24551240.21726982822100
5.9217-7.45150.28051300.226627192849100
7.4515-38.13290.21471560.19792666282294

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