[English] 日本語
Yorodumi
- PDB-8qkt: Structure of a nucleosome composed of a palindromic 167-base pair... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 H3.1
  • Histone H4
KeywordsDNA / nucleosome / histone / chromatin
Function / homology
Function and homology information


nucleosomal DNA binding / 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 / 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 ...nucleosomal DNA binding / 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 / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / gene expression / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / extracellular space / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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


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


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

-
Components

-
Protein , 4 types, 12 molecules AAAEEEKKKOOOBBBFFFLLLPPPCCCMMMGGGQQQ

#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: 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

-
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

-
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)

-
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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more