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- EMDB-10390: Structure of a human nucleosome at 3.2 A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-10390
TitleStructure of a human nucleosome at 3.2 A resolution
Map data
SampleNucleosome:
ProteinsProtein / DNA / Histone H3.2 / Histone H4 / Histone H2A type 1-B/E / Histone H2B type 1-K / (nucleic-acidNucleic acid) x 2
Function / homology
Function and homology information


negative regulation of megakaryocyte differentiation / Packaging Of Telomere Ends / depurination / positive regulation of histone exchange / CENP-A containing chromatin assembly / Chromatin modifying enzymes / 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 DNA recombination at telomere ...negative regulation of megakaryocyte differentiation / Packaging Of Telomere Ends / depurination / positive regulation of histone exchange / CENP-A containing chromatin assembly / Chromatin modifying enzymes / 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 DNA recombination at telomere / DNA replication-independent chromatin assembly / telomere capping / Inhibition of DNA recombination at telomere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / interleukin-7-mediated signaling pathway / Meiotic synapsis / heterochromatin assembly => GO:0031507 / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / DNA replication-dependent chromatin assembly / DNA methylation / HCMV Late Events / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / rDNA heterochromatin assembly / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / negative regulation of gene expression, epigenetic / RNA Polymerase I Promoter Escape / mitotic chromosome condensation / regulation of gene silencing by miRNA / HDACs deacetylate histones / nuclear chromosome / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / regulation of megakaryocyte differentiation / B-WICH complex positively regulates rRNA expression / DNA-templated transcription, initiation / Metalloprotease DUBs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / nucleosome assembly / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / RMTs methylate histone arginines / HCMV Early Events / regulation of androgen receptor signaling pathway / Pre-NOTCH Transcription and Translation / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / nucleosome / Activation of anterior HOX genes in hindbrain development during early embryogenesis / UCH proteinases / Transcriptional regulation of granulopoiesis / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / double-strand break repair / double-strand break repair via nonhomologous end joining / chromatin organization / Processing of DNA double-strand break ends / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromosome, telomeric region / viral life cycle / killing of cells of other organism / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / antimicrobial humoral immune response mediated by antimicrobial peptide / Ub-specific processing proteases / blood coagulation / protein ubiquitination / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / amyloid fibril formation / protein domain specific binding / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus / 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 2A / Histone H2A / Histone H4, conserved site ...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 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / 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 H2B type 1-K / Histone H2A type 1-B/E / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDodonova SO / Zhu F / Dienemann C / Taipale J / Cramer P
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Research Council693023 Germany
Volkswagen Foundation Germany
European Molecular Biology OrganizationALTF-949-2016 Germany
CitationJournal: Nature / Year: 2020
Title: Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Authors: Svetlana O Dodonova / Fangjie Zhu / Christian Dienemann / Jussi Taipale / Patrick Cramer /
Abstract: 'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions ...'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.
History
DepositionOct 21, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseApr 29, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t79
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10390.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 140 pix.
= 147. Å
1.05 Å/pix.
x 140 pix.
= 147. Å
1.05 Å/pix.
x 140 pix.
= 147. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.07724066 - 0.16049513
Average (Standard dev.)0.0009965262 (±0.009815395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 147.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z147.000147.000147.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.0770.1600.001

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Supplemental data

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Half map: half-map 2, nucleosome

Fileemd_10390_half_map_1.map
Annotationhalf-map 2, nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half-map 1, nucleosome

Fileemd_10390_half_map_2.map
Annotationhalf-map 1, nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Nucleosome

EntireName: Nucleosome / Details: Nucleosome / Number of Components: 9

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Component #1: protein, Nucleosome

ProteinName: Nucleosome / Details: Nucleosome / Recombinant expression: No
MassTheoretical: 205 kDa

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Component #2: protein, Proteins

ProteinName: ProteinsProtein / Details: ProteinsProtein / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, DNA

ProteinName: DNA / Details: DNA / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Histone H3.2

ProteinName: Histone H3.2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.389036 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #6: protein, Histone H2A type 1-B/E

ProteinName: Histone H2A type 1-B/E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.707277 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #7: protein, Histone H2B type 1-K

ProteinName: Histone H2B type 1-K / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.921213 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #8: nucleic-acid, DNA (147-MER)

nucleic acidName: DNA (147-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC)(DG)(DA) (DC)(DG)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG) (DA)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DT)(DA) (DT)(DG)(DT)(DT)(DT)(DG)(DT)(DT)(DA)(DG) (DC)(DG)(DT)(DT)(DA)(DT) ...Sequence:
(DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC)(DG)(DA) (DC)(DG)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG) (DA)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DT)(DA) (DT)(DG)(DT)(DT)(DT)(DG)(DT)(DT)(DA)(DG) (DC)(DG)(DT)(DT)(DA)(DT)(DA)(DC)(DT)(DA) (DT)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DC)(DT) (DT)(DT)(DG)(DT)(DT)(DT)(DC)(DG)(DG)(DT) (DG)(DG)(DT)(DA)(DT)(DT)(DG)(DT)(DT)(DT) (DA)(DT)(DT)(DT)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DT)(DT)(DG)(DT)(DG)(DC)(DG)(DT)(DT) (DC)(DA)(DG)(DC)(DT)(DT)(DA)(DA)(DT)(DG) (DC)(DC)(DT)(DA)(DA)(DC)(DG)(DA)(DC)(DA) (DC)(DT)(DC)(DG)(DG)(DA)(DG)(DA)(DT)(DC) (DG)(DG)(DA)(DA)(DG)(DA)(DG)(DC)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DA)(DT)
MassTheoretical: 45.240848 kDa
SourceSpecies: synthetic construct (others)

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Component #9: nucleic-acid, DNA (147-MER)

nucleic acidName: DNA (147-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DG) (DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG)(DT) (DC)(DG)(DT)(DT)(DA)(DG)(DG)(DC)(DA)(DT) (DT)(DA)(DA)(DG)(DC)(DT) ...Sequence:
(DA)(DT)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DG) (DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG)(DT) (DC)(DG)(DT)(DT)(DA)(DG)(DG)(DC)(DA)(DT) (DT)(DA)(DA)(DG)(DC)(DT)(DG)(DA)(DA)(DC) (DG)(DC)(DA)(DC)(DA)(DA)(DA)(DG)(DG)(DA) (DA)(DC)(DA)(DA)(DA)(DA)(DT)(DA)(DA)(DA) (DC)(DA)(DA)(DT)(DA)(DC)(DC)(DA)(DC)(DC) (DG)(DA)(DA)(DA)(DC)(DA)(DA)(DA)(DG)(DA) (DA)(DT)(DT)(DA)(DG)(DA)(DA)(DT)(DA)(DG) (DT)(DA)(DT)(DA)(DA)(DC)(DG)(DC)(DT)(DA) (DA)(DC)(DA)(DA)(DA)(DC)(DA)(DT)(DA)(DA) (DA)(DT)(DT)(DA)(DG)(DA)(DT)(DC)(DG)(DG) (DA)(DA)(DG)(DA)(DG)(DC)(DG)(DT)(DC)(DG) (DT)(DG)(DT)(DA)(DG)(DA)(DT)
MassTheoretical: 45.484273 kDa
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/mL / pH: 7.5
Support film0.39 mB, 25 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 289 K / Humidity: 100 %
Details: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen ...Details: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: At least 50% of the data were collected at 25* stage tilt in order to partially compensate for preferred orientation of particles on the grid, and to improve angular distribution.
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 1.125 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 130000 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1000.0 - 3500.0 nm / Energy Filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 368270
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 6FQ5
Overall BValue: 75
Output model

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