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- PDB-6l9h: The Human Telomeric Nucleosome Displays Distinct Structural and D... -

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Basic information

Entry
Database: PDB / ID: 6l9h
TitleThe Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties
Components
  • (Human Telomeric DNA (145-MER) - ...) x 2
  • Histone H2A type 1-B/E
  • Histone H2B type 1-K
  • Histone H3.1
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / Telomeric DNA / Nucleosome Core Particle / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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 / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...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 / 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 / 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 / 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 / chloroplast / 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 / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / 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 / HCMV Early Events / structural constituent of chromatin / UCH proteinases / nucleosome / heterochromatin formation / 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) / small ribosomal subunit rRNA binding / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / ribosome / structural constituent of ribosome / cadherin binding / translation / protein heterodimerization activity / Amyloid fiber formation / ribonucleoprotein complex / negative regulation of cell population proliferation / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
Histone, subunit A / Histone, subunit A / 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, subunit A / Histone, subunit A / 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. / Ribosomal protein S6, plastid/chloroplast / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Translation elongation factor EF1B/ribosomal protein S6 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Small ribosomal subunit protein bS6c alpha / Histone H2A type 1-B/E / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSoman, A. / Liew, C.W. / Teo, H.L. / Berezhnoy, N. / Korolev, N. / Rhodes, D. / Nordenskiold, L.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: The human telomeric nucleosome displays distinct structural and dynamic properties.
Authors: Soman, A. / Liew, C.W. / Teo, H.L. / Berezhnoy, N.V. / Olieric, V. / Korolev, N. / Rhodes, D. / Nordenskiold, L.
History
DepositionNov 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.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-K
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-K
I: Human Telomeric DNA (145-MER) - G-strand
J: Human Telomeric DNA (145-MER) - C-strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,47414
Polymers176,25410
Non-polymers2204
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57410 Å2
ΔGint-401 kcal/mol
Surface area72390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.455, 109.388, 176.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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


Mass: 11269.213 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) / References: UniProt: P68431
#2: Protein Histone H4


Mass: 9990.770 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) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A


Mass: 11508.419 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) / References: UniProt: P04908
#4: Protein Histone H2B type 1-K / Histone H2B


Mass: 10607.174 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) / References: UniProt: O60814

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Human Telomeric DNA (145-MER) - ... , 2 types, 2 molecules IJ

#5: DNA chain Human Telomeric DNA (145-MER) - G-strand


Mass: 46024.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#6: DNA chain Human Telomeric DNA (145-MER) - C-strand


Mass: 43478.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 10 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.518→92.961 Å / Num. obs: 33289 / % possible obs: 94.5 % / Redundancy: 13 % / Biso Wilson estimate: 70.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Rrim(I) all: 0.119 / Net I/σ(I): 14.3
Reflection shellResolution: 2.518→2.899 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.506 / Num. unique obs: 1665 / CC1/2: 0.795 / Rpim(I) all: 0.426 / Rrim(I) all: 1.567 / % possible all: 79.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
PDB_EXTRACT3.25data extraction
autoPROCdata collection
XDSdata reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZ0

3lz0


Resolution: 2.6→46 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.534
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 1620 4.88 %RANDOM
Rwork0.2363 ---
obs0.2384 33177 51.8 %-
Displacement parametersBiso max: 200.83 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-1.4979 Å20 Å20 Å2
2---2.9775 Å20 Å2
3---1.4796 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 2.6→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 5939 4 6 11931
Biso mean--131.76 13.82 -
Num. residues----1043
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3703SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1308HARMONIC5
X-RAY DIFFRACTIONt_it12721HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1667SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6884SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12721HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg18420HARMONIC20.76
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion24.62
LS refinement shellResolution: 2.6→3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2623 26 3.92 %
Rwork0.265 638 -
all0.2649 664 -
obs--6.51 %

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