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- EMDB-17251: Structure of apo telomeric nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-17251
TitleStructure of apo telomeric nucleosome
Map dataPostprocess map of Apo-TeloNCP
Sample
  • Complex: TRF1core in complex with telomeric nucleosome
    • Complex: Human telomeric nucleosome
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-C
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • DNA: Telomeric DNA G strand
      • DNA: Telomeric DNA C strand
  • Ligand: water
KeywordsTelomeric nucleosome / shelterin / telomere / DNA BINDING PROTEIN
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 / innate immune response in mucosa / 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / 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 / identical protein binding / 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
Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Histone H2A type 1-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsHu H / van Roon AMM / Ghanim GE / Ahsan B / Oluwole A / Peak-Chew S / Robinson CV / Nguyen THD
Funding support United Kingdom, European Union, United States, 3 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/19 United Kingdom
European Molecular Biology Organization (EMBO)European Union
Jane Coffin Childs (JCC) Fund United States
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis of telomeric nucleosome recognition by shelterin factor TRF1.
Authors: Hongmiao Hu / Anne-Marie M van Roon / George E Ghanim / Bilal Ahsan / Abraham O Oluwole / Sew-Yeu Peak-Chew / Carol V Robinson / Thi Hoang Duong Nguyen /
Abstract: Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We ...Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We report cryo-electron microscopy structures of a human telomeric nucleosome both unbound and bound to the shelterin factor TRF1. Our structures reveal that TRF1 binds unwrapped nucleosomal DNA ends by engaging both the nucleosomal DNA and the histone octamer. Unexpectedly, TRF1 binding shifts the register of the nucleosomal DNA by 1 bp. We discovered that phosphorylation of the TRF1 C terminus and a noncanomical DNA binding surface on TRF1 are critical for its association with telomeric nucleosomes. These insights into shelterin-chromatin interactions have crucial implications for understanding telomeric chromatin organization and other roles of shelterin at telomeres including replication and transcription.
History
DepositionApr 28, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17251.png

Downloads & links

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Map

FileDownload / File: emd_17251.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocess map of Apo-TeloNCP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 300 pix.
= 219. Å		0.73 Å/pix.
x 300 pix.
= 219. Å		0.73 Å/pix.
x 300 pix.
= 219. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.009175153 - 0.026127283
Average (Standard dev.)-0.00017241582 (±0.0010129738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 219.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Refine3D map of Apo-TeloNCP

Fileemd_17251_additional_1.map
AnnotationRefine3D map of Apo-TeloNCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refine3D half map of Apo-TeloNCP

Fileemd_17251_half_map_1.map
AnnotationRefine3D half map of Apo-TeloNCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refine3D half map of Apo-TeloNCP

Fileemd_17251_half_map_2.map
AnnotationRefine3D half map of Apo-TeloNCP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRF1core in complex with telomeric nucleosome

EntireName: TRF1core in complex with telomeric nucleosome
Components
  • Complex: TRF1core in complex with telomeric nucleosome
    • Complex: Human telomeric nucleosome
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-C
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • DNA: Telomeric DNA G strand
      • DNA: Telomeric DNA C strand
  • Ligand: water

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Supramolecule #1: TRF1core in complex with telomeric nucleosome

SupramoleculeName: TRF1core in complex with telomeric nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Human telomeric nucleosome

SupramoleculeName: Human telomeric nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Details: Human telomeric nucleosome with 145 bp DNA and human histone octamer. 145 bp DNA consists of 23 copies of TTAGGG repeats. Histone octamer consists of 2 copies of H2A, H2B, H3 and H4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.805581 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRGMARTKQ TARKSTGGKA PRKQLATKAA RKSAPATGGV KKPHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRF QSSAVMALQE ACEAYLVGLF EDTNLCAIHA KRVTIMPKDI QLARRIRGER A

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.762839 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRGMSGRGK GGKGLGKGGA KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAM DVVYALKRQG RTLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-C

MacromoleculeName: Histone H2A type 1-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.503938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRGMSGRGK QGGKARAKAK SRSSRAGLQF PVGRVHRLLR KGNYAERVGA GAPVYLAAVL EYLTAEILEL AGNAARDNKK TRIIPRHLQ LAIRNDEELN KLLGRVTIAQ GGVLPNIQAV LLPKKTESHH KAKGK

UniProtKB: Histone H2A type 1-C

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.305627 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRGMPEPAK SAPAPKKGSK KAVTKAQKKD GKKRKRSRKE SYSVYVYKVL KQVHPDTGIS SKAMGIMNSF VNDIFERIAG EASRLAHYN KRSTITSREI QTAVRLLLPG ELAKHAVSEG TKAVTKYTSS K

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #5: Telomeric DNA G strand

MacromoleculeName: Telomeric DNA G strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.024258 KDa
SequenceString: (DA)(DT)(DC)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT) (DT)(DA)(DG)(DG)(DG)(DT) ...String:
(DA)(DT)(DC)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DG) (DA)(DT)

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Macromolecule #6: Telomeric DNA C strand

MacromoleculeName: Telomeric DNA C strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.478914 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA) (DC)(DC)(DC)(DT)(DA)(DA) ...String:
(DA)(DT)(DC)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DG) (DA)(DT)

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 57 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMKClPotassium chloride
25.0 mMC8H18N2O4SHEPES
1.0 mMMgCl2Magnesium chloride
1.0 %C3H8O3glycerol
0.01 %(C2H4O)nC14H22OIgepal CA-630
1.0 mMC4H10O2S2Dithiothreitol

Details: 25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630,1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot Force: -15 Blot Time: 2.5 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12126 / Average exposure time: 1.15 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsAll images were processed using RELION4.0
Particle selectionNumber selected: 5031654
Startup modelType of model: EMDB MAP
EMDB ID:

25481


Details: 2.6 A structure of the nucleosome from a class without Chd1
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66482
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX (ver. 1.5)
Output model

PDB-8ox0:
Structure of apo telomeric nucleosome

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