[English] 日本語
Yorodumi
- PDB-6ke9: The Human Telomeric Nucleosome Displays Distinct Structural and D... -

+
Open data


ID or keywords:

Loading...

-
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 H3.1Histone H3
  • 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 / 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 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 / 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 / SUMOylation of chromatin organization proteins / 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) / 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 / Metalloprotease DUBs / 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 / UCH proteinases / 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 / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / 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 / membrane / nucleus / cytosol
Similarity search - Function
Histone, subunit A / Histone, subunit A / 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, subunit A / Histone, subunit A / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.1 / Histone H3


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

-
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)

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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