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- PDB-5y0c: Crystal Structure of the human nucleosome at 2.09 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5y0c
TitleCrystal Structure of the human nucleosome at 2.09 angstrom resolution
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / DNA binding / nucleus / histone fold / chromatin formation / nucleosome / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / DNA replication-independent nucleosome assembly / telomere capping / interleukin-7-mediated signaling pathway / chromatin silencing / telomere organization / DNA replication-dependent nucleosome assembly / nucleosome => GO:0000786 ...negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / DNA replication-independent nucleosome assembly / telomere capping / interleukin-7-mediated signaling pathway / chromatin silencing / telomere organization / DNA replication-dependent nucleosome assembly / nucleosome => GO:0000786 / innate immune response in mucosa / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing / regulation of gene silencing by miRNA / nuclear chromosome / DNA-templated transcription, initiation / regulation of megakaryocyte differentiation / nucleosome assembly / lipopolysaccharide binding / nucleosome / double-strand break repair via nonhomologous end joining / chromosome, telomeric region => GO:0000781 / chromatin organization / killing of cells of other organism / antibacterial humoral response / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / protein ubiquitination / cadherin binding / defense response to Gram-negative bacterium / protein heterodimerization activity / defense response to Gram-positive bacterium / chromatin => GO:0000785 / negative regulation of cell population proliferation / protein domain specific binding / cellular protein metabolic process / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus / cytosol
CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Histone H4, conserved site / Histone-fold / Histone H2A/H2B/H3 / TATA box binding protein associated factor (TAF) / Histone H2A / Histone H4 / Histone H2B ...CENP-T/Histone H4, histone fold / Histone H2A conserved site / Histone H2A, C-terminal domain / Histone H4, conserved site / Histone-fold / Histone H2A/H2B/H3 / TATA box binding protein associated factor (TAF) / Histone H2A / Histone H4 / Histone H2B / Histone H3/CENP-A / Histone, subunit A / Histone, subunit A / Orthogonal Bundle / Mainly Alpha
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.087 Å
AuthorsKurumizaka, H. / Arimura, Y. / Fujita, R. / Noda, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPSJP17K15043 Japan
JSPSJP25116002 Japan
JP16J10043 Japan
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome.
Authors: Arimura, Y. / Ikura, M. / Fujita, R. / Noda, M. / Kobayashi, W. / Horikoshi, N. / Sun, J. / Shi, L. / Kusakabe, M. / Harata, M. / Ohkawa, Y. / Tashiro, S. / Kimura, H. / Ikura, T. / Kurumizaka, H.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (146-MER)
J: DNA (146-MER)
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,92224
Polymers202,23110
Non-polymers69114
Water7,062392
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58550 Å2
ΔGint-492 kcal/mol
Surface area72440 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)98.913, 107.103, 167.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain E
12chain B
22chain F
13chain C
23chain G
14chain D
24chain H
15chain I
25chain J

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA38 - 1370
211chain EE36 - 1409
112chain BB25 - 101
212chain FF16 - 1399
113chain CC11 - 1391
213chain GG15 - 1360
114chain DD32 - 1395
214chain HH33 - 1398
115chain II2 - 1413
215chain JJ147 - 1392

NCS ensembles:
ID
1
2
3
4
5

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Components

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DNA chain , 1 types, 2 molecules IJ

#1: 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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Protein , 4 types, 8 molecules AEBFCGDH

#2: 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: 15719.445 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: pH3.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68431
#3: 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: pH4 / Cell (production host): JM109(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#4: 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) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Plasmid: pH2A / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#5: 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) / Gene: HIST1H2BJ, H2BFR / Plasmid: pH2B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06899

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Non-polymers , 3 types, 406 molecules

#6: Chemical
ChemComp-MN / MANGANESE (II) ION / Manganese


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
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-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 25, 2014
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.08→20 Å / Num. obs: 103710 / % possible obs: 98.5 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.032 / Rrim(I) all: 0.105 / Χ2: 1.004 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.08-2.155.40.4870.6850.2070.5320.92191.2
2.15-2.2460.4340.7740.1780.4710.97197
2.24-2.346.40.370.8580.1490.4011.01999
2.34-2.476.40.3220.9010.1310.3491.04999.3
2.47-2.627.80.2550.9570.0920.2721.07599.5
2.62-2.828.20.1990.9780.070.2121.05799.4
2.82-3.19.40.1370.9940.0450.1450.96499.7
3.1-3.5511.50.0830.9980.0240.0860.97599.9
3.55-4.4711.80.0720.9980.0220.0760.99299.9
4.47-20130.0860.9970.0240.0891.009100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å20.06 Å
Translation3 Å20.06 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.5phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CV5

2cv5


Resolution: 2.087→20 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.84
RfactorNum. reflection% reflection
Rfree0.2492 1991 1.92 %
Rwork0.2019 --
Obs0.2028 103642 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.8 Å2 / Biso mean: 40.9244 Å2 / Biso min: 13.99 Å2
Refinement stepCycle: final / Resolution: 2.087→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 5962 14 392 12368
Biso mean--43.48 33.23 -
Num. residues----1045
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefinement-IDRmsType
11A932X-RAY DIFFRACTION5.689TORSIONAL
12E932X-RAY DIFFRACTION5.689TORSIONAL
21B724X-RAY DIFFRACTION5.689TORSIONAL
22F724X-RAY DIFFRACTION5.689TORSIONAL
31C976X-RAY DIFFRACTION5.689TORSIONAL
32G976X-RAY DIFFRACTION5.689TORSIONAL
41D834X-RAY DIFFRACTION5.689TORSIONAL
42H834X-RAY DIFFRACTION5.689TORSIONAL
51I2894X-RAY DIFFRACTION5.689TORSIONAL
52J2894X-RAY DIFFRACTION5.689TORSIONAL

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