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- PDB-6jr0: Crystal structure of the human nucleosome phased with 12 selenium... -

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Basic information

Entry
Database: PDB / ID: 6jr0
TitleCrystal structure of the human nucleosome phased with 12 selenium atoms
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsGENE REGULATION/DNA / nucleosome / chromatin / histone / selenomethionine / SAD phasing / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine ...protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / antibacterial humoral response / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Centromere kinetochore component CENP-T histone fold ...Histone, subunit A / Histone, subunit A / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Centromere kinetochore component CENP-T histone fold / 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 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 H2A type 1-B/E / Histone H2B type 1-J / Arachidonate 15-lipoxygenase / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSaotome, M. / Horikoshi, N. / Urano, K. / Kujirai, T. / Yuzurihara, H. / Kurumizaka, H. / Kagawa, W.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP24570138 Japan
Japan Society for the Promotion of ScienceJP26116521 Japan
Japan Society for the Promotion of ScienceJP16H01316 Japan
Japan Society for the Promotion of ScienceJP18H05534 Japan
Japan Society for the Promotion of ScienceJP17H01408 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structure determination of the nucleosome core particle by selenium SAD phasing.
Authors: Saotome, M. / Horikoshi, N. / Urano, K. / Kujirai, T. / Yuzurihara, H. / Kurumizaka, H. / Kagawa, W.
History
DepositionApr 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: DNA (146-MER)
J: DNA (146-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,72822
Polymers203,14710
Non-polymers58112
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58150 Å2
ΔGint-488 kcal/mol
Surface area72580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.566, 108.514, 168.935
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/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: 15860.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(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)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
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: 14559.655 Da / Num. of mol.: 2 / Mutation: L65M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14423.137 Da / Num. of mol.: 2 / Mutation: L106M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Plasmid: pHCE / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P06899

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DNA chain , 1 types, 2 molecules IJ

#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) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 455 molecules

#6: Chemical
ChemComp-CL / CHLORIDE ION


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.: 8 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 21, 2016
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→49.02 Å / Num. obs: 64077 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.052 / Rrim(I) all: 0.142 / Net I/σ(I): 13.8
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 4451 / CC1/2: 0.923 / Rpim(I) all: 0.289 / Rrim(I) all: 0.767 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→49.015 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.2
RfactorNum. reflection% reflection
Rfree0.2533 3195 4.99 %
Rwork0.2212 --
obs0.2228 63988 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 5980 12 443 12424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512778
X-RAY DIFFRACTIONf_angle_d0.77818503
X-RAY DIFFRACTIONf_dihedral_angle_d24.8466682
X-RAY DIFFRACTIONf_chiral_restr0.0432100
X-RAY DIFFRACTIONf_plane_restr0.0061330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53730.34011360.27742605X-RAY DIFFRACTION100
2.5373-2.5770.35611470.28112607X-RAY DIFFRACTION100
2.577-2.61920.29561250.26272622X-RAY DIFFRACTION100
2.6192-2.66440.31621180.272616X-RAY DIFFRACTION100
2.6644-2.71280.34981590.27222586X-RAY DIFFRACTION100
2.7128-2.7650.28311550.27872621X-RAY DIFFRACTION100
2.765-2.82150.41341260.28442598X-RAY DIFFRACTION100
2.8215-2.88280.29491270.27982617X-RAY DIFFRACTION100
2.8828-2.94980.29351280.27562652X-RAY DIFFRACTION100
2.9498-3.02360.30791340.27062624X-RAY DIFFRACTION100
3.0236-3.10530.29421370.26032615X-RAY DIFFRACTION100
3.1053-3.19670.27291430.25212623X-RAY DIFFRACTION100
3.1967-3.29990.30041570.24342599X-RAY DIFFRACTION100
3.2999-3.41780.27471430.23182627X-RAY DIFFRACTION100
3.4178-3.55460.24881310.21532642X-RAY DIFFRACTION100
3.5546-3.71630.22791380.21592650X-RAY DIFFRACTION100
3.7163-3.91220.25951500.20962631X-RAY DIFFRACTION100
3.9122-4.15710.2261460.1922646X-RAY DIFFRACTION100
4.1571-4.47790.2131470.17922655X-RAY DIFFRACTION100
4.4779-4.92820.21631650.18662657X-RAY DIFFRACTION100
4.9282-5.64040.17211150.18792706X-RAY DIFFRACTION100
5.6404-7.10290.21061460.20562725X-RAY DIFFRACTION100
7.1029-49.02480.18821220.17422869X-RAY DIFFRACTION100

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