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- PDB-8qkt: Structure of a nucleosome composed of a palindromic 167-base pair... -

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Entry
Database: PDB / ID: 8qkt
TitleStructure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment
Components
  • (DNA (167-MER)) x 2
  • (Histone H2A) x 2
  • (Histone H2B type 1- ...) x 2
  • Histone H3.1Histone H3
  • Histone H4
KeywordsDNA / nucleosome / histone / chromatin
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / 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 ...negative regulation of tumor necrosis factor-mediated signaling pathway / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / 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 / Interleukin-7 signaling / 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 / 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 / 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 / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / 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 / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
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 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
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2A / Histone H4 / Histone H2A / Histone H2B type 1-J / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.261 Å
AuthorsMa, Z. / Davey, C.A.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
Citation
Journal: To Be Published
Title: Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment
Authors: Ma, Z. / Davey, C.A.
#1: Journal: Nucleic Acids Res / Year: 2021
Title: Engineering nucleosomes for generating diverse chromatin assemblies.
Authors: Adhireksan, Z. / Sharma, D. / Lee, P.L. / Bao, Q. / Padavattan, S. / Shum, W.K. / Davey, G.E. / Davey, C.A.
History
DepositionSep 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Histone H3.1
BBB: Histone H4
CCC: Histone H2A
DDD: Histone H2B type 1-J
EEE: Histone H3.1
FFF: Histone H4
GGG: Histone H2A
HHH: Histone H2B type 1-J
III: DNA (167-MER)
JJJ: DNA (167-MER)
KKK: Histone H3.1
LLL: Histone H4
MMM: Histone H2A
NNN: Histone H2B type 1-J
OOO: Histone H3.1
PPP: Histone H4
QQQ: Histone H2A
RRR: Histone H2B type 1-J
SSS: DNA (167-MER)
TTT: DNA (167-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,67553
Polymers376,86220
Non-polymers1,81333
Water0
1
AAA: Histone H3.1
BBB: Histone H4
CCC: Histone H2A
DDD: Histone H2B type 1-J
EEE: Histone H3.1
FFF: Histone H4
GGG: Histone H2A
HHH: Histone H2B type 1-J
III: DNA (167-MER)
JJJ: DNA (167-MER)
hetero molecules


  • defined by author
  • Evidence: native gel electrophoresis
  • 189 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)189,47529
Polymers188,43110
Non-polymers1,04419
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61040 Å2
ΔGint-480 kcal/mol
Surface area79590 Å2
2
KKK: Histone H3.1
LLL: Histone H4
MMM: Histone H2A
NNN: Histone H2B type 1-J
OOO: Histone H3.1
PPP: Histone H4
QQQ: Histone H2A
RRR: Histone H2B type 1-J
SSS: DNA (167-MER)
TTT: DNA (167-MER)
hetero molecules


  • defined by author
  • 189 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)189,20024
Polymers188,43110
Non-polymers76914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60330 Å2
ΔGint-458 kcal/mol
Surface area79720 Å2
Unit cell
Length a, b, c (Å)108.437, 103.722, 185.405
Angle α, β, γ (deg.)90.000, 93.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 12 molecules AAAEEEKKKOOOBBBFFFLLLPPPCCCMMMGGGQQQ

#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: 11504.476 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein
Histone H4 /


Mass: 8910.394 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8C1JQV0
#3: Protein Histone H2A /


Mass: 11508.419 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC8 / Production host: Escherichia coli (E. coli) / References: UniProt: H2QSF5
#5: Protein Histone H2A /


Mass: 11308.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LOC102977259 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Y9FT95

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Histone H2B type 1- ... , 2 types, 4 molecules DDDNNNHHHRRR

#4: Protein Histone H2B type 1-J


Mass: 10778.394 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11 / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#6: Protein Histone H2B type 1-J


Mass: 10907.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11 / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

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DNA chain , 2 types, 4 molecules IIISSSJJJTTT

#7: DNA chain DNA (167-MER)


Mass: 51553.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#8: DNA chain DNA (167-MER)


Mass: 51544.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 33 molecules

#9: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Mn

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Details

Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: MnCl2-containing buffers

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.26→48.66 Å / Num. obs: 61655 / % possible obs: 96 % / Redundancy: 3.2 % / CC1/2: 0.997 / Net I/σ(I): 8.9
Reflection shellResolution: 3.26→3.44 Å / Num. unique obs: 7836 / CC1/2: 0.541

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.261→48.655 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.79 / Cross valid method: FREE R-VALUE / ESU R Free: 0.76
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.321 2865 5.001 %
Rwork0.2692 54426 -
all0.272 --
obs-57291 89.061 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 88.517 Å2
Baniso -1Baniso -2Baniso -3
1--2.504 Å20 Å2-0.466 Å2
2---1.818 Å2-0 Å2
3---4.346 Å2
Refinement stepCycle: LAST / Resolution: 3.261→48.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11980 13682 33 0 25695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01227488
X-RAY DIFFRACTIONr_bond_other_d0.0270.01819702
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.37439994
X-RAY DIFFRACTIONr_angle_other_deg2.2962.13545834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.06451492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.4918.539712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.373152312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.95415172
X-RAY DIFFRACTIONr_chiral_restr0.0930.23604
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0221486
X-RAY DIFFRACTIONr_gen_planes_other0.0030.026136
X-RAY DIFFRACTIONr_nbd_refined0.1780.24795
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.220063
X-RAY DIFFRACTIONr_nbtor_refined0.2110.211460
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.210799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2329
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0450.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.28
X-RAY DIFFRACTIONr_nbd_other0.2490.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.22
X-RAY DIFFRACTIONr_mcbond_it2.3517.0066016
X-RAY DIFFRACTIONr_mcbond_other2.3517.0056015
X-RAY DIFFRACTIONr_mcangle_it4.11510.4837492
X-RAY DIFFRACTIONr_mcangle_other4.11510.4857493
X-RAY DIFFRACTIONr_scbond_it2.75810.49321472
X-RAY DIFFRACTIONr_scbond_other2.75810.49321471
X-RAY DIFFRACTIONr_scangle_it4.71715.78932502
X-RAY DIFFRACTIONr_scangle_other4.71615.78932503
X-RAY DIFFRACTIONr_lrange_it7.70399.64734575
X-RAY DIFFRACTIONr_lrange_other7.70399.64634574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.261-3.3450.3611770.34333530.34447070.6350.68474.99470.34
3.345-3.4370.3452130.3240570.32145970.710.72892.88670.315
3.437-3.5360.3412130.29240400.29444400.7570.79195.78830.283
3.536-3.6440.4271070.37620450.37943350.6660.71249.64240.409
3.644-3.7630.788750.79414450.79342100.5310.47636.10450.817
3.763-3.8940.3951960.38336960.38440620.7040.69395.81490.37
3.894-4.040.441900.37436130.37739530.7140.73396.20540.33
4.04-4.2040.2911890.23735710.2437730.8590.8899.65540.207
4.204-4.3890.2911810.21734470.22136370.8690.89899.75250.192
4.389-4.6010.2451730.19832930.20134720.9020.91599.82720.172
4.601-4.8480.2351660.18731570.18933240.9160.93399.96990.16
4.848-5.1390.2241580.1930010.19231650.9250.92899.81040.162
5.139-5.4890.2751470.18327890.18829460.8910.92499.66060.158
5.489-5.9230.2591370.19226010.19627450.9120.92599.7450.164
5.923-6.4780.2791290.224370.20425710.8930.92199.80550.171
6.478-7.2270.3131150.21221910.21723070.8720.90699.95670.182
7.227-8.3150.2411020.17519440.17920530.9340.94999.6590.158
8.315-10.110.23880.17916570.18117630.9320.94998.9790.169
10.11-13.9980.202680.15213050.15413820.9530.96499.34880.159
13.998-48.6550.246410.2027830.2048540.9490.95496.48710.217

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