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- EMDB-29841: Human Oct4 bound to nucleosome with human nMatn1 sequence (focuse... -

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Basic information

Entry
Database: EMDB / ID: EMD-29841
TitleHuman Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of Oct4 bound region)
Map dataOct4 from composite map of Oct4 bound to nucleosome with human nMatn1 sequence
Sample
  • Complex: Nucleosome with Human nMatn1 sequence
    • DNA: nMatn1 DNA (top strand)
    • DNA: nMatn1 DNA (bottom strand)
    • Protein or peptide: POU domain, class 5, transcription factor 1
KeywordsOct4 / Nucleosome / Pioneer factor / nMatn1 DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / Specification of primordial germ cells / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation ...cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / Specification of primordial germ cells / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / Transcriptional regulation of pluripotent stem cells / Germ layer formation at gastrulation / miRNA binding / somatic stem cell population maintenance / blastocyst development / anatomical structure morphogenesis / BMP signaling pathway / negative regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / regulation of gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / Homeobox, conserved site / 'Homeobox' domain signature. ...POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
POU domain, class 5, transcription factor 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 Å
AuthorsSinha KK / Bilokapic S / Du Y / Malik D / Halic M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM135599-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM141694-01 United States
CitationJournal: Nature / Year: 2023
Title: Histone modifications regulate pioneer transcription factor cooperativity.
Authors: Kalyan K Sinha / Silvija Bilokapic / Yongming Du / Deepshikha Malik / Mario Halic /
Abstract: Pioneer transcription factors have the ability to access DNA in compacted chromatin. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation ...Pioneer transcription factors have the ability to access DNA in compacted chromatin. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation between the pioneer transcription factors OCT4 (also known as POU5F1) and SOX2 is important for pluripotency and reprogramming. However, the molecular mechanisms by which pioneer transcription factors function and cooperate on chromatin remain unclear. Here we present cryo-electron microscopy structures of human OCT4 bound to a nucleosome containing human LIN28B or nMATN1 DNA sequences, both of which bear multiple binding sites for OCT4. Our structural and biochemistry data reveal that binding of OCT4 induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional OCT4 and of SOX2 to their internal binding sites. The flexible activation domain of OCT4 contacts the N-terminal tail of histone H4, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA-binding domain of OCT4 engages with the N-terminal tail of histone H3, and post-translational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our findings suggest that the epigenetic landscape could regulate OCT4 activity to ensure proper cell programming.
History
DepositionFeb 17, 2023-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29841.png

Downloads & links

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Map

FileDownload / File: emd_29841.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOct4 from composite map of Oct4 bound to nucleosome with human nMatn1 sequence
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 200 pix.
= 322. Å		1.61 Å/pix.
x 200 pix.
= 322. Å		1.61 Å/pix.
x 200 pix.
= 322. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.61 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.043278214 - 0.11967481
Average (Standard dev.)0.000018115792 (±0.0014016543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29841_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29841_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleosome with Human nMatn1 sequence

EntireName: Nucleosome with Human nMatn1 sequence
Components
  • Complex: Nucleosome with Human nMatn1 sequence
    • DNA: nMatn1 DNA (top strand)
    • DNA: nMatn1 DNA (bottom strand)
    • Protein or peptide: POU domain, class 5, transcription factor 1

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Supramolecule #1: Nucleosome with Human nMatn1 sequence

SupramoleculeName: Nucleosome with Human nMatn1 sequence / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: nMatn1 DNA (top strand)

MacromoleculeName: nMatn1 DNA (top strand) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.93359 KDa
SequenceString: (DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC) (DA)(DT)(DG)(DC)(DT)(DA)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DG) (DG) (DT)(DT)(DA)(DA)(DT)(DA) ...String:
(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC) (DA)(DT)(DG)(DC)(DT)(DA)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA) (DA)(DT)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DG) (DG) (DT)(DT)(DA)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC)(DA)(DC)(DA)(DT)(DA)(DC)(DA) (DC)(DA) (DC)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DA) (DC)(DA)(DC)(DA)(DT)(DA) (DT)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DT)(DG) (DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DC) (DA)(DC)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG) (DC)(DG)(DC)(DA)(DC)(DA) (DT)(DA)(DG) (DT)(DC)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DT) (DG)(DC)(DA)(DC)(DA)(DC)(DA) (DT)(DT) (DA)(DG)(DC)(DA)(DT)(DA)(DT)(DG)(DC)(DA) (DT)(DA)(DC)(DA)(DC)(DA)(DT)(DA) (DC) (DA)(DT)(DG)(DC)(DA)

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Macromolecule #2: nMatn1 DNA (bottom strand)

MacromoleculeName: nMatn1 DNA (bottom strand) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.889855 KDa
SequenceString: (DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DG)(DT)(DA)(DT)(DG)(DC)(DA)(DT)(DA) (DT)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT) (DG) (DT)(DG)(DA)(DC)(DT)(DA) ...String:
(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DG)(DT)(DA)(DT)(DG)(DC)(DA)(DT)(DA) (DT)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT) (DG) (DT)(DG)(DA)(DC)(DT)(DA)(DT)(DG) (DT)(DG)(DC)(DG)(DC)(DA)(DT)(DG)(DC)(DA) (DT)(DG) (DT)(DG)(DC)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DA)(DT) (DA)(DC)(DG) (DT)(DG)(DT)(DG)(DT)(DG) (DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DT)(DG) (DC)(DA)(DT)(DA) (DT)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT) (DG)(DT)(DG)(DT)(DG) (DC)(DA)(DT)(DG) (DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA)(DT)(DG) (DT)(DG)(DT)(DA)(DT)(DA) (DT)(DA)(DT) (DT)(DA)(DA)(DC)(DC)(DT)(DG)(DT)(DG)(DT) (DG)(DC)(DA)(DT)(DT)(DG)(DT) (DG)(DT) (DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT)(DT)(DA) (DG)(DC)(DA)(DT)(DG)(DT)(DG)(DT) (DG) (DC)(DA)(DT)(DG)(DT)

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Macromolecule #3: POU domain, class 5, transcription factor 1

MacromoleculeName: POU domain, class 5, transcription factor 1 / type: protein_or_peptide / ID: 3 / Details: Human Oct4 bound to nMatn1 DNA / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.299453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSSHHHHHHS SGLVPRGSHM ASMTGGQQMG RDPNSMAGHL ASDFAFSPPP GGGGDGPGGP EPGWVDPRTW LSFQGPPGGP GIGPGVGPG SEVWGIPPCP PPYEFCGGMA YCGPQVGVGL VPQGGLETSQ PEGEAGVGVE SNSDGASPEP CTVTPGAVKL E KEKLEQNP ...String:
GSSHHHHHHS SGLVPRGSHM ASMTGGQQMG RDPNSMAGHL ASDFAFSPPP GGGGDGPGGP EPGWVDPRTW LSFQGPPGGP GIGPGVGPG SEVWGIPPCP PPYEFCGGMA YCGPQVGVGL VPQGGLETSQ PEGEAGVGVE SNSDGASPEP CTVTPGAVKL E KEKLEQNP EESQDIKALQ KELEQFAKLL KQKRITLGYT QADVGLTLGV LFGKVFSQTT ICRFEALQLS FKNMCKLRPL LQ KWVEEAD NNENLQEICK AETLVQARKR KRTSIENRVR GNLENLFLQC PKPTLQQISH IAQQLGLEKD VVRVWFCNRR QKG KRSSSD YAQREDFEAA GSPFSGGPVS FPLAPGPHFG TPGYGSPHFT ALYSSVPFPE GEAFPPVSVT TLGSPMHSN

UniProtKB: POU domain, class 5, transcription factor 1

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
1.0 mMC4H10O2S2DTT

Details: 50 mM HEPES pH 7.5, 1 mM DTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21970

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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