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- EMDB-10406: OCT4-SOX2-bound nucleosome - SHL-6 -

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Basic information

Entry
Database: EMDB / ID: EMD-10406
TitleOCT4-SOX2-bound nucleosome - SHL-6
Map data
SampleTernary complex of OCT4-SOX2 and SHL-6 nucleosome
  • HistonesHistone
  • DNA
  • G protein/GFP fusion protein,POU domain, class 5, transcription factor 1 (OCT4)
  • SOX2
  • (Histone H3.1Histone H3) x 2
  • Histone H4
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • (nucleic-acidNucleic acid) x 2
  • Green fluorescent protein,POU domain, class 5, transcription factor 1
  • Transcription factor SOX-2
  • ligand
Function / homology
Function and homology information


regulation of heart induction by regulation of canonical Wnt signaling pathway / cell fate commitment involved in formation of primary germ layer / regulation of DNA methylation-dependent heterochromatin assembly / glial cell fate commitment / cardiac cell fate determination / regulation of asymmetric cell division / endodermal cell fate specification / BMP signaling pathway involved in heart induction / adenohypophysis development / positive regulation of cell-cell adhesion ...regulation of heart induction by regulation of canonical Wnt signaling pathway / cell fate commitment involved in formation of primary germ layer / regulation of DNA methylation-dependent heterochromatin assembly / glial cell fate commitment / cardiac cell fate determination / regulation of asymmetric cell division / endodermal cell fate specification / BMP signaling pathway involved in heart induction / adenohypophysis development / positive regulation of cell-cell adhesion / regulation of cysteine-type endopeptidase activity involved in apoptotic process / pituitary gland development / neuronal stem cell population maintenance / eye development / response to growth factor / tissue regeneration / blastocyst development / miRNA binding / somatic stem cell population maintenance / negative regulation of gene silencing by miRNA / positive regulation of SMAD protein signal transduction / negative regulation of pri-miRNA transcription by RNA polymerase II / negative regulation of megakaryocyte differentiation / inner ear development / depurination / positive regulation of histone exchange / CENP-A containing nucleosome assembly / negative regulation of tumor necrosis factor-mediated signaling pathway / anatomical structure morphogenesis / negative regulation of DNA recombination at telomere / negative regulation of neuron differentiation / DNA replication-independent nucleosome assembly / telomere capping / interleukin-7-mediated signaling pathway / cell fate commitment / chromatin silencing / telomere organization / DNA replication-dependent nucleosome assembly / forebrain development / innate immune response in mucosa / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / regulation of gene silencing / mitotic chromosome condensation / bioluminescence / regulation of gene silencing by miRNA / osteoblast differentiation / positive regulation of cell differentiation / generation of precursor metabolites and energy / nuclear chromosome / DNA-templated transcription, initiation / regulation of megakaryocyte differentiation / nucleosome assembly / lipopolysaccharide binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of androgen receptor signaling pathway / nucleosome / response to wounding / regulation of cell cycle => GO:0051726 / positive regulation of canonical Wnt signaling pathway / negative regulation of canonical Wnt signaling pathway / transcription regulator complex / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / double-strand break repair / chromatin organization / double-strand break repair via nonhomologous end joining / protein-chromophore linkage / positive regulation of MAPK cascade / chromosome, telomeric region / viral life cycle / DNA-binding transcription activator activity, RNA polymerase II-specific / killing of cells of other organism / antibacterial humoral response / sequence-specific DNA binding / regulation of gene expression / transcription cis-regulatory region binding / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / protein ubiquitination / cadherin binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to Gram-negative bacterium / protein heterodimerization activity / defense response to Gram-positive bacterium / negative regulation of cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / DNA-binding transcription factor activity / transcription factor binding / amyloid fibril formation / protein domain specific binding / cytokine-mediated signaling pathway / ubiquitin protein ligase binding / regulation of transcription, DNA-templated / regulation of transcription by RNA polymerase II / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II
Homeobox-like domain superfamily / Histone-fold / High mobility group box domain / Green fluorescent protein-related / POU domain-containing protein, class 5 / Homeobox, conserved site / Histone H4, conserved site / Lambda repressor-like, DNA-binding domain superfamily / Transcription factor SOX / Histone H2A, C-terminal domain ...Homeobox-like domain superfamily / Histone-fold / High mobility group box domain / Green fluorescent protein-related / POU domain-containing protein, class 5 / Homeobox, conserved site / Histone H4, conserved site / Lambda repressor-like, DNA-binding domain superfamily / Transcription factor SOX / Histone H2A, C-terminal domain / Histone H2A conserved site / Transcription factor SOX-2 / CENP-T/Histone H4, histone fold / High mobility group box domain superfamily / POU domain / Green fluorescent protein, GFP / Histone H2A/H2B/H3 / Histone H3/CENP-A / POU-specific domain / Histone H2B / Green fluorescent protein / Homeobox domain / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF)
Histone H2A type 1-B/E / Histone H2B type 1-J / Green fluorescent protein / Transcription factor SOX-2 / Histone H4 / Histone H3.1 / POU domain, class 5, transcription factor 1
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsMichael AK / Kempf G / Cavadini S / Bunker RD / Thoma NH
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII3_160734/1 Switzerland
CitationJournal: Science / Year: 2020
Title: Mechanisms of OCT4-SOX2 motif readout on nucleosomes.
Authors: Alicia K Michael / Ralph S Grand / Luke Isbel / Simone Cavadini / Zuzanna Kozicka / Georg Kempf / Richard D Bunker / Andreas D Schenk / Alexandra Graff-Meyer / Ganesh R Pathare / Joscha ...Authors: Alicia K Michael / Ralph S Grand / Luke Isbel / Simone Cavadini / Zuzanna Kozicka / Georg Kempf / Richard D Bunker / Andreas D Schenk / Alexandra Graff-Meyer / Ganesh R Pathare / Joscha Weiss / Syota Matsumoto / Lukas Burger / Dirk Schübeler / Nicolas H Thomä /
Abstract: Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors ...Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo-electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionOct 25, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseMay 6, 2020-
UpdateJul 8, 2020-
Current statusJul 8, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t90
  • Surface level: 0.15
  • 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_10406.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å
0.86 Å/pix.
x 256 pix.
= 220.16 Å
0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.44070667 - 1.0866412
Average (Standard dev.)0.0072323447 (±0.049836557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z220.160220.160220.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.4411.0870.007

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Supplemental data

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Sample components

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Entire Ternary complex of OCT4-SOX2 and SHL-6 nucleosome

EntireName: Ternary complex of OCT4-SOX2 and SHL-6 nucleosome / Number of components: 15

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Component #1: protein, Ternary complex of OCT4-SOX2 and SHL-6 nucleosome

ProteinName: Ternary complex of OCT4-SOX2 and SHL-6 nucleosome / Recombinant expression: No

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Component #2: protein, Histones

ProteinName: HistonesHistone / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #3: protein, DNA

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

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Component #4: protein, G protein/GFP fusion protein,POU domain, class 5, transc...

ProteinName: G protein/GFP fusion protein,POU domain, class 5, transcription factor 1 (OCT4)
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, SOX2

ProteinName: SOX2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: protein, Histone H3.1

ProteinName: Histone H3.1Histone H3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.719445 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #7: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.676703 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #8: protein, Histone H2A type 1-B/E

ProteinName: Histone H2A type 1-B/E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.447825 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #9: protein, Histone H2B type 1-J

ProteinName: Histone H2B type 1-J / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.088336 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #10: protein, Histone H3.1

ProteinName: Histone H3.1Histone H3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.491173 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #11: nucleic-acid, DNA (146-MER)

nucleic acidName: DNA (146-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DT)(DT)(DG)(DT)(DT)(DA)(DT)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DC)(DG)(DC)(DT) (DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA) ...Sequence:
(DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DT)(DT)(DG)(DT)(DT)(DA)(DT)(DG) (DC)(DA)(DA)(DA)(DT)(DC)(DC)(DG)(DC)(DT) (DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC) (DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC) (DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT) (DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT) (DG)(DA)(DT)
MassTheoretical: 46.961957 kDa
SourceSpecies: synthetic construct (others)

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Component #12: nucleic-acid, DNA (146-MER)

nucleic acidName: DNA (146-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC) ...Sequence:
(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DA)(DT)(DT)(DT)(DG) (DC)(DA)(DT)(DA)(DA)(DC)(DA)(DA)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA)(DG)
MassTheoretical: 45.634125 kDa
SourceSpecies: synthetic construct (others)

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Component #13: protein, Green fluorescent protein,POU domain, class 5, transcrip...

ProteinName: Green fluorescent protein,POU domain, class 5, transcription factor 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 70.521289 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #14: protein, Transcription factor SOX-2

ProteinName: Transcription factor SOX-2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.718679 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #15: ligand, PENTANEDIAL

LigandName: PENTANEDIALGlutaraldehyde / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.100116 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 94282
3D reconstructionSoftware: cryoSPARC / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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