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- PDB-6ke9: The Human Telomeric Nucleosome Displays Distinct Structural and D... -

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Basic information

Entry
Database: PDB / ID: 6ke9
TitleThe Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties
Components
  • Histone H2A type 1-B/E
  • Histone H2B type 1-K
  • Histone H3.1
  • Histone H4
  • Human Telomeric DNA (145-MER)
  • Human telomeric DNA (145-MER)
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 / Inhibition of DNA recombination at telomere / telomere organization / 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) / 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 / epigenetic regulation of gene expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / 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 / HCMV Early Events / Transcriptional regulation of granulopoiesis / heterochromatin formation / nucleosome assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / gene expression / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / 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, subunit A / Histone, subunit A / : / 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, subunit A / Histone, subunit A / : / 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 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H2B type 1-K / 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: 2.22 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
DepositionJul 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / refine / refine_ls_shell
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 / _refine.ls_percent_reflns_obs / _refine_ls_shell.percent_reflns_obs
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)
J: Human Telomeric DNA (145-MER)
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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57020 Å2
ΔGint-406 kcal/mol
Surface area73320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.133, 109.319, 176.969
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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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain Human telomeric DNA (145-MER)


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)


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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
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: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→93 Å / Num. obs: 53570 / % possible obs: 99.3 % / Redundancy: 13.2 % / Biso Wilson estimate: 62.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.012 / Net I/σ(I): 26.1
Reflection shellResolution: 2.18→2.22 Å / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5306 / CC1/2: 0.81 / Rpim(I) all: 0.343

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Processing

Software
NameVersionClassification
autoPROCdata scaling
BUSTER2.10.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZ0

3lz0


Resolution: 2.22→42.01 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.35
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2337 5.36 %RANDOM
Rwork0.204 ---
obs0.205 43634 42.1 %-
Displacement parametersBiso max: 249.58 Å2 / Biso mean: 128.26 Å2 / Biso min: 11.87 Å2
Baniso -1Baniso -2Baniso -3
1-11.0167 Å20 Å20 Å2
2---26.0055 Å20 Å2
3---14.9888 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.22→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 5939 4 6 11931
Biso mean--142.42 30.34 -
Num. residues----1043
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3707SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1308HARMONIC5
X-RAY DIFFRACTIONt_it12721HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
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_contact12801SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12721HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg18420HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion24.31
LS refinement shellResolution: 2.22→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3739 45 5.15 %
Rwork0.2451 828 -
all0.2515 873 -
obs--5.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5121-0.14310.39897.47320.7964.127-0.00560.4233-0.456-2.1637-0.17561.2157-0.13450.21290.18120.30780.0477-0.4362-0.6707-0.00460.03524.94926.9093-56.3961
23.47391.03990.29918.5151-0.26844.11870.0144-0.0525-0.3699-0.5995-0.10341.23220.04550.00250.089-0.12110.0192-0.1986-0.670.02650.14133.007721.7232-47.8977
32.94330.45520.72887.8351-1.64692.67630.0064-0.3188-0.64760.9352-0.2202-1.78760.70921.01650.2138-0.32470.1185-0.2574-0.49980.08350.227630.783118.1329-32.4031
47.18911.11290.44887.9954-1.22954.63570.1652-0.4341-0.55541.6522-0.2424-1.23470.50850.53710.07720.17380.0273-0.3412-0.5170.1552-0.121124.709118.522-24.8426
52.65960.4704-0.43553.81840.58434.692-0.34640.42090.0283-1.11960.1038-2.042-0.26331.32440.2427-0.3345-0.0620.4361-0.35590.160.435637.948935.4943-51.2717
63.5633-0.27140.23036.37840.55964.6231-0.24750.14910.1957-0.42590.0018-2.0293-0.40011.24720.2457-0.4104-0.15370.0922-0.34880.10470.43235.647239.8224-44.0309
73.51130.02531.58328.7393-0.26511.7753-0.2547-0.26970.20850.1349-0.14341.099-0.42-0.13130.3981-0.1108-0.0232-0.1033-0.57630.030.10735.790347.4299-38.9633
84.3321.29842.14888.03541.19375.47530.0329-0.56310.33691.0673-0.2210.8649-0.2569-0.11860.18810.0573-0.04610.0466-0.5333-0.0505-0.0258.966548.1589-30.4193
92.36540.23330.45549.68170.96722.35020.1058-0.2282-0.2148-0.7485-0.1662-0.3261-0.14340.34020.0603-0.8572-0.0368-0.0238-1.38590.1309-0.922819.117831.9243-41.2046
101.9021-0.28960.316310.06050.0432.08790.0985-0.0677-0.0489-0.8997-0.2808-0.1647-0.1520.30020.1823-0.9203-0.0473-0.052-1.23230.0378-0.909219.047232.4777-41.3955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A40 - 134
2X-RAY DIFFRACTION2{ B|* }B16 - 102
3X-RAY DIFFRACTION3{ C|* }C16 - 118
4X-RAY DIFFRACTION4{ D|* }D28 - 122
5X-RAY DIFFRACTION5{ E|* }E40 - 135
6X-RAY DIFFRACTION6{ F|* }F25 - 102
7X-RAY DIFFRACTION7{ G|* }G14 - 118
8X-RAY DIFFRACTION8{ H|* }H28 - 121
9X-RAY DIFFRACTION9{ I|* }I4 - 7
10X-RAY DIFFRACTION10{ J|* }J1 - 6

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