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- PDB-6ler: 169 bp nucleosome harboring non-identical cohesive DNA termini. -

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Basic information

Entry
Database: PDB / ID: 6ler
Title169 bp nucleosome harboring non-identical cohesive DNA termini.
Components
  • (DNA (169-MER)) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsDNA BINDING PROTEIN / Nucleosome / DNA-protein complex / DNA BINDING PROTEIN-DNA complex / Linker Histone / H1.0
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / innate immune response in mucosa / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / 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 / 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 / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / antimicrobial humoral immune response mediated by antimicrobial peptide / HCMV Early Events / structural constituent of chromatin / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / 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) / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / gene expression / killing of cells of another organism / Estrogen-dependent gene expression / chromosome, telomeric region / 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 / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / 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 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 / 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 / Histone-fold
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
other sequences (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSharma, D. / Adhireksan, Z. / Lee, P.L. / Davey, C.A.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) Singapore
CitationJournal: 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
DepositionNov 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Histone H3.1
L: Histone H4
M: Histone H2A type 1-B/E
N: Histone H2B type 1-J
O: Histone H3.1
P: Histone H4
Q: Histone H2A type 1-B/E
R: Histone H2B type 1-J
S: DNA (169-MER)
T: DNA (169-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
I: DNA (169-MER)
J: DNA (169-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)429,08537
Polymers428,40720
Non-polymers67817
Water45025
1
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 (169-MER)
J: DNA (169-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,52218
Polymers214,20310
Non-polymers3198
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60160 Å2
ΔGint-440 kcal/mol
Surface area79560 Å2
MethodPISA
2
K: Histone H3.1
L: Histone H4
M: Histone H2A type 1-B/E
N: Histone H2B type 1-J
O: Histone H3.1
P: Histone H4
Q: Histone H2A type 1-B/E
R: Histone H2B type 1-J
S: DNA (169-MER)
T: DNA (169-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,56319
Polymers214,20310
Non-polymers3609
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60800 Å2
ΔGint-426 kcal/mol
Surface area79230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.338, 116.545, 117.900
Angle α, β, γ (deg.)61.500, 82.770, 64.230
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 16 molecules KOAELPBFMQCGNRDH

#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: 15437.167 Da / Num. of mol.: 4
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.: 4
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.: 4
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.: 4
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, 4 molecules SJTI

#5: DNA chain DNA (169-MER)


Mass: 52330.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) other sequences (unknown) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (169-MER)


Mass: 52008.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) other sequences (unknown) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 42 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Calcium chloride, potassium chloride, sodium acetate

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Data collection

DiffractionMean temperature: 98.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.12 Å / Num. obs: 88754 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.056 / Rrim(I) all: 0.079 / Net I/σ(I): 12
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1 / Num. unique obs: 4306 / CC1/2: 0.539 / Rpim(I) all: 0.883 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ut9

3ut9


Resolution: 3→48.12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1778 2 %RANDOM
Rwork0.2084 ---
obs0.2094 86975 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 327.1 Å2 / Biso mean: 118.078 Å2 / Biso min: 47.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å2-2.53 Å20.73 Å2
2---2.66 Å21.91 Å2
3---1.41 Å2
Refinement stepCycle: final / Resolution: 3→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12007 13862 17 25 25911
Biso mean--130.42 69.41 -
Num. residues----2189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01227715
X-RAY DIFFRACTIONr_bond_other_d0.0270.01819813
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.37440344
X-RAY DIFFRACTIONr_angle_other_deg2.3212.13846104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03351497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95918.612706
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.971152319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.58415169
X-RAY DIFFRACTIONr_chiral_restr0.0630.23633
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221647
X-RAY DIFFRACTIONr_gen_planes_other0.0050.026198
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 118 -
Rwork0.341 6117 -
all-6235 -
obs--94.07 %

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