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Open data
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Basic information
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Title | Genomic CX3CR1 nucleosome | |||||||||
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![]() | nucleosome / transcription factor / transcription / chromatin binding protein-DNA complex / DNA 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: 2.6 Å | |||||||||
![]() | Lian T / Guan R / Bai Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα. Authors: Tengfei Lian / Ruifang Guan / Bing-Rui Zhou / Yawen Bai / ![]() Abstract: Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA ...Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA targets remains elusive. Here we report the structures of the nucleosome containing the mouse genomic CX3CR1 enhancer DNA and its complexes with PU.1 alone and with both PU.1 and the C/EBPα DNA binding domain. Our structures reveal that PU.1 binds the DNA motif at the exit linker, shifting 17 bp of DNA into the core region through interactions with H2A, unwrapping ~20 bp of nucleosomal DNA. C/EBPα binding, aided by PU.1's repositioning, unwraps ~25 bp of entry DNA. The PU.1 Q218H mutation, linked to acute myeloid leukemia, disrupts PU.1-H2A interactions. PU.1 and C/EBPα jointly displace linker histone H1 and open the H1-condensed nucleosome array. Our study unveils how two pioneer factors can work cooperatively to open closed chromatin by altering DNA positioning in the nucleosome. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 26.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.1 KB 20.1 KB | Display Display | ![]() |
Images | ![]() | 37.3 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 49 MB 49 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sypMC ![]() 8evhC ![]() 8eviC ![]() 8evjC 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
-Half map: #2
File | emd_40889_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40889_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : free CX3CR1 nucleosome
Entire | Name: free CX3CR1 nucleosome |
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Components |
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-Supramolecule #1: free CX3CR1 nucleosome
Supramolecule | Name: free CX3CR1 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 UniProtKB: Histone H3.1 |
-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 UniProtKB: Arachidonate 15-lipoxygenase |
-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 UniProtKB: Histone H2A type 2-C |
-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 UniProtKB: Histone H2B type 2-E |
-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: 50.043855 KDa |
Sequence | String: (DT)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DG)(DC) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG) (DC)(DT)(DG)(DA)(DG)(DA) ...String: (DT)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DG)(DC) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG) (DC)(DT)(DG)(DA)(DG)(DA)(DG)(DT) (DT)(DG)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DG) (DC)(DT) (DG)(DA)(DG)(DT)(DC)(DT)(DT) (DA)(DG)(DC)(DA)(DA)(DT)(DG)(DG)(DA)(DT) (DA)(DC)(DT) (DT)(DC)(DC)(DC)(DG)(DA) (DT)(DT)(DC)(DC)(DC)(DC)(DT)(DC)(DA)(DC) (DA)(DA)(DA)(DA) (DA)(DT)(DA)(DG)(DG) (DT)(DC)(DA)(DG)(DT)(DC)(DT)(DG)(DT)(DC) (DT)(DG)(DG)(DC)(DT) (DA)(DG)(DT)(DT) (DC)(DT)(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DC) (DA)(DG)(DA)(DC)(DA)(DC) (DA)(DG)(DG) (DG)(DC)(DA)(DT)(DG)(DT)(DG)(DG)(DG)(DG) (DT)(DT)(DC)(DC)(DT)(DA)(DT) (DT)(DT) GENBANK: GENBANK: DQ360291.1 |
-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: 49.965957 KDa |
Sequence | String: (DA)(DA)(DA)(DT)(DA)(DG)(DG)(DA)(DA)(DC) (DC)(DC)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DC) (DC)(DT)(DG)(DT)(DG)(DT)(DC)(DT)(DG) (DC)(DA)(DA)(DG)(DT)(DA)(DC)(DA)(DG)(DA) (DA) (DC)(DT)(DA)(DG)(DC)(DC) ...String: (DA)(DA)(DA)(DT)(DA)(DG)(DG)(DA)(DA)(DC) (DC)(DC)(DC)(DA)(DC)(DA)(DT)(DG)(DC)(DC) (DC)(DT)(DG)(DT)(DG)(DT)(DC)(DT)(DG) (DC)(DA)(DA)(DG)(DT)(DA)(DC)(DA)(DG)(DA) (DA) (DC)(DT)(DA)(DG)(DC)(DC)(DA)(DG) (DA)(DC)(DA)(DG)(DA)(DC)(DT)(DG)(DA)(DC) (DC)(DT) (DA)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DG)(DA)(DG)(DG)(DG)(DG)(DA)(DA)(DT) (DC)(DG)(DG) (DG)(DA)(DA)(DG)(DT)(DA) (DT)(DC)(DC)(DA)(DT)(DT)(DG)(DC)(DT)(DA) (DA)(DG)(DA)(DC) (DT)(DC)(DA)(DG)(DC) (DA)(DA)(DT)(DG)(DC)(DT)(DG)(DC)(DA)(DA) (DC)(DT)(DC)(DT)(DC) (DA)(DG)(DC)(DA) (DA)(DC)(DC)(DA)(DG)(DC)(DT)(DG)(DA)(DA) (DG)(DA)(DT)(DC)(DA)(DG) (DC)(DA)(DG) (DC)(DC)(DG)(DA)(DG)(DA)(DG)(DG)(DC)(DC) (DC)(DT)(DG)(DC)(DA)(DC)(DC) (DT)(DA) GENBANK: GENBANK: DQ360291.1 |
-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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143066 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |