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- PDB-5xf3: Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-... -

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Basic information

Entry
Database: PDB / ID: 5xf3
TitleNucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration)
Components
  • (DNA (145-MER)) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1Histone H3
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / Nucleosome / Histone adduct / Ruthenium compound / Binuclear metal-based agent / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / Packaging Of Telomere Ends / Chromatin modifying enzymes / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / DNA replication-independent chromatin assembly / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / Packaging Of Telomere Ends / Chromatin modifying enzymes / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / DNA replication-independent chromatin assembly / 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 / heterochromatin assembly => GO:0031507 / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Interleukin-7 signaling / DNA replication-dependent chromatin assembly / DNA methylation / innate immune response in mucosa / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / 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 / DNA-templated transcription, initiation / Metalloprotease DUBs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / lipopolysaccharide binding / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / RMTs methylate histone arginines / nucleosome assembly / HCMV Early Events / HDMs demethylate histones / Pre-NOTCH Transcription and Translation / Meiotic recombination / PKMTs methylate histone lysines / nucleosome / Activation of anterior HOX genes in hindbrain development during early embryogenesis / UCH proteinases / Transcriptional regulation of granulopoiesis / 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) / chromosome, telomeric region / killing of cells of another organism / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / 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 signature. / Histone H2A conserved site / 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 signature. / Histone H2A conserved site / 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 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / 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 H4 / Histone H2B type 1-J / Histone H2A type 1-B/E / (1R,2R)-1,2-diphenylethane-1,2-diamine / Chem-RUD / DNA (> 100) / DNA (> 10) / DNA / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMa, Z. / Adhireksan, Z. / Murray, B.S. / Dyson, P.J. / Davey, C.A.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore
CitationJournal: Nat Commun / Year: 2017
Title: Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation
Authors: Davey, G.E. / Adhireksan, Z. / Ma, Z. / Riedel, T. / Sharma, D. / Padavattan, S. / Rhodes, D. / Ludwig, A. / Sandin, S. / Murray, B.S. / Dyson, P.J. / Davey, C.A.
History
DepositionApr 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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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 (145-MER)
J: DNA (145-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,67415
Polymers199,35510
Non-polymers1,3195
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57210 Å2
ΔGint-399 kcal/mol
Surface area73580 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)108.190, 109.400, 174.820
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: 15437.167 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
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein Histone H4 /


Mass: 11394.426 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
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14165.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13935.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (145-MER)


Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 5 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-RUD / [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2


Mass: 493.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24Cl2N3O2PRu
#9: Chemical ChemComp-RRK / (1R,2R)-1,2-diphenylethane-1,2-diamine


Mass: 212.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2
#10: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Details

Nonpolymer detailsThe dinuclear ruthenium antitumour compound [(R,R)-DPEN linker, trans conformation] is composed of ...The dinuclear ruthenium antitumour compound [(R,R)-DPEN linker, trans conformation] is composed of RUD-RRK-RUD. RUD-RRK-RUD form the complete ligand and are linked with peptide bonds.

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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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.5 Å
DetectorType: PSI PILATUS 6M / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.6→58.27 Å / Num. obs: 64455 / % possible obs: 99.9 % / Redundancy: 5.8 % / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.505 / % possible all: 99.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MNN
Resolution: 2.6→52.748 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.791 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27017 1303 2 %RANDOM
Rwork0.23458 ---
obs0.23534 63050 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 105.554 Å2
Baniso -1Baniso -2Baniso -3
1-9.65 Å2-0 Å20 Å2
2---7.35 Å20 Å2
3----2.31 Å2
Refinement stepCycle: 1 / Resolution: 2.6→52.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 5939 66 0 12099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01512916
X-RAY DIFFRACTIONr_bond_other_d0.0030.029686
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.54918723
X-RAY DIFFRACTIONr_angle_other_deg1.292322426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45421.255271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.142151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6231586
X-RAY DIFFRACTIONr_chiral_restr0.0810.21829
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210321
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022864
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7077.5363056
X-RAY DIFFRACTIONr_mcbond_other5.6997.5333055
X-RAY DIFFRACTIONr_mcangle_it8.15611.2683806
X-RAY DIFFRACTIONr_mcangle_other8.15511.2723807
X-RAY DIFFRACTIONr_scbond_it7.89912.4569860
X-RAY DIFFRACTIONr_scbond_other7.89512.4549857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.89218.66414864
X-RAY DIFFRACTIONr_long_range_B_refined16.01616590
X-RAY DIFFRACTIONr_long_range_B_other16.01516591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 92 -
Rwork0.368 4559 -
obs--99.06 %

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