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- EMDB-29846: Human Oct4 bound to nucleosome with human LIN28B sequence -

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Basic information

Entry
Database: EMDB / ID: EMD-29846
TitleHuman Oct4 bound to nucleosome with human LIN28B sequence
Map data
Sample
  • Complex: Human Oct4 bound to a Nucleosome with human LIN28 DNA sequence
    • DNA: LIN28B DNA (32-MER)
    • DNA: LIN28B DNA (32-MER)
    • Protein or peptide: POU domain, class 5, transcription factor 1
KeywordsOct4 / Nucleosome / LIN28B DNA / iPSC / 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 / Transcriptional regulation of pluripotent stem cells / regulation of DNA methylation-dependent heterochromatin formation / 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 / positive regulation of canonical Wnt signaling pathway / sequence-specific double-stranded DNA binding / regulation of gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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. / Homeodomain ...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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29846.png

Downloads & links

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Map

FileDownload / File: emd_29846.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.014811228 - 0.077017464
Average (Standard dev.)-0.00004494371 (±0.0018807704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29846_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_29846_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Oct4 bound to a Nucleosome with human LIN28 DNA sequence

EntireName: Human Oct4 bound to a Nucleosome with human LIN28 DNA sequence
Components
  • Complex: Human Oct4 bound to a Nucleosome with human LIN28 DNA sequence
    • DNA: LIN28B DNA (32-MER)
    • DNA: LIN28B DNA (32-MER)
    • Protein or peptide: POU domain, class 5, transcription factor 1

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Supramolecule #1: Human Oct4 bound to a Nucleosome with human LIN28 DNA sequence

SupramoleculeName: Human Oct4 bound to a Nucleosome with human LIN28 DNA sequence
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: LIN28B DNA (32-MER)

MacromoleculeName: LIN28B DNA (32-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.519281 KDa
SequenceString: (DG)(DC)(DA)(DT)(DA)(DA)(DG)(DT)(DT)(DA) (DA)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT) (DC)(DA)(DG)(DT)(DG)(DG)(DT)(DG)(DA)(DG) (DT) (DA)(DT)(DT)(DA)(DA)(DC) ...String:
(DG)(DC)(DA)(DT)(DA)(DA)(DG)(DT)(DT)(DA) (DA)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT) (DC)(DA)(DG)(DT)(DG)(DG)(DT)(DG)(DA)(DG) (DT) (DA)(DT)(DT)(DA)(DA)(DC)(DA)(DT) (DG)(DG)(DA)(DA)(DC)(DT)(DT)(DA)(DC)(DT) (DC)(DC) (DA)(DA)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DG)(DA)(DT)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DA) (DA)(DA)(DT)(DG)(DT)(DA) (DG)(DT)(DC)(DT)(DA)(DA)(DG)(DT)(DG)(DA) (DA)(DG)(DA)(DA) (DA)(DG)(DA)(DA)(DG) (DG)(DA)(DA)(DA)(DG)(DG)(DT)(DG)(DG)(DG) (DA)(DG)(DC)(DT)(DG) (DC)(DC)(DA)(DT) (DC)(DA)(DC)(DT)(DC)(DA)(DG)(DA)(DA)(DT) (DT)(DG)(DT)(DC)(DC)(DA) (DG)(DC)(DA) (DG)(DG)(DG)(DA)(DT)(DT)(DG)(DT)(DG)(DC) (DA)(DA)(DG)(DC)(DT)(DT)(DG) (DT)(DG) (DA)(DA)(DT)(DA)(DA)(DA)(DG)(DA)(DC)(DA) (DC)(DA)(DT)(DA)(DC)(DT)(DT)(DC) (DA) (DT)

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Macromolecule #2: LIN28B DNA (32-MER)

MacromoleculeName: LIN28B DNA (32-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.827664 KDa
SequenceString: (DA)(DT)(DG)(DA)(DA)(DG)(DT)(DA)(DT)(DG) (DT)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DC)(DA)(DA)(DG)(DC)(DT)(DT) (DG)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(DC) (DT) (DG)(DC)(DT)(DG)(DG)(DA) ...String:
(DA)(DT)(DG)(DA)(DA)(DG)(DT)(DA)(DT)(DG) (DT)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DC)(DA)(DA)(DG)(DC)(DT)(DT) (DG)(DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(DC) (DT) (DG)(DC)(DT)(DG)(DG)(DA)(DC)(DA) (DA)(DT)(DT)(DC)(DT)(DG)(DA)(DG)(DT)(DG) (DA)(DT) (DG)(DG)(DC)(DA)(DG)(DC)(DT) (DC)(DC)(DC)(DA)(DC)(DC)(DT)(DT)(DT)(DC) (DC)(DT)(DT) (DC)(DT)(DT)(DT)(DC)(DT) (DT)(DC)(DA)(DC)(DT)(DT)(DA)(DG)(DA)(DC) (DT)(DA)(DC)(DA) (DT)(DT)(DT)(DA)(DT) (DT)(DC)(DA)(DG)(DC)(DA)(DT)(DC)(DT)(DG) (DT)(DA)(DT)(DT)(DG) (DT)(DT)(DG)(DG) (DA)(DG)(DT)(DA)(DA)(DG)(DT)(DT)(DC)(DC) (DA)(DT)(DG)(DT)(DT)(DA) (DA)(DT)(DA) (DC)(DT)(DC)(DA)(DC)(DC)(DA)(DC)(DT)(DG) (DA)(DG)(DG)(DA)(DT)(DA)(DT) (DG)(DT) (DT)(DA)(DA)(DT)(DA)(DC)(DC)(DA)(DC)(DT) (DT)(DA)(DA)(DC)(DT)(DT)(DA)(DT) (DG) (DC)

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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 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 90.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21970

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65000

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