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Open data
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Basic information
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Title | Structure of 162bp LIN28b nucleosome | |||||||||
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![]() | nucleosome / transcription factor / transcription / CHROMATIN BINDING PROTEIN-DNA complex / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | ![]() Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes ...Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / HCMV Late Events / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / antibacterial humoral response / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Lian T / Guan R / Bai Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mechanism of LIN28B nucleosome targeting by OCT4. Authors: Ruifang Guan / Tengfei Lian / Bing-Rui Zhou / David Wheeler / Yawen Bai / ![]() Abstract: Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of ...Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.9 KB 15.9 KB | Display Display | ![]() |
Images | ![]() | 54.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u0jMC ![]() 7u0gC ![]() 7u0iC ![]() 8dk5C ![]() 8spsC ![]() 8spuC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Native nucleosome
Entire | Name: Native nucleosome |
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Components |
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-Supramolecule #1: Native nucleosome
Supramolecule | Name: Native nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.437167 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG |
-Macromolecule #3: Histone H2A type 2-C
Macromolecule | Name: Histone H2A type 2-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.017428 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHKAKSK |
-Macromolecule #4: Histone H2B type 2-E
Macromolecule | Name: Histone H2B type 2-E / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.951239 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK |
-Macromolecule #7: Single-chain variable fragment
Macromolecule | Name: Single-chain variable fragment / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 29.030146 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ...String: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ASLGERVTIT CKASQDIRSY LSWYQQKPWK SPKTLIYYAT SLADGVPSRF SGSGSGQDFS LTINNLESDD TA TYYCLQH GESPYTFGSG TKLEIKRA |
-Macromolecule #5: DNA (162-MER)
Macromolecule | Name: DNA (162-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 50.398344 KDa |
Sequence | String: (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) ...String: (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)(DG)(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) |
-Macromolecule #6: DNA (162-MER)
Macromolecule | Name: DNA (162-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 49.59568 KDa |
Sequence | String: (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) ...String: (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)(DC)(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) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 359203 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |