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Yorodumi- EMDB-28630: CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28630 | |||||||||
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Title | CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations | |||||||||
Map data | ||||||||||
Sample |
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Keywords | nucleosome / transcription factor / transcription / chromatin binding protein-DNA complex / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | Function and homology information positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity ...positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / granulocyte differentiation / lymphocyte differentiation / apoptotic process involved in blood vessel morphogenesis / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation / immature B cell differentiation / negative regulation of MHC class II biosynthetic process / lymphoid progenitor cell differentiation / myeloid dendritic cell differentiation / vasculature development / regulation of DNA-binding transcription factor activity / oncogene-induced cell senescence / negative regulation of protein localization to chromatin / positive regulation of p38MAPK cascade / positive regulation of B cell differentiation / NFAT protein binding / somatic stem cell population maintenance / macrophage differentiation / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / cis-regulatory region sequence-specific DNA binding / 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 / lipopolysaccharide-mediated signaling pathway / nucleosomal DNA binding / protein sequestering activity / 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 / transcription initiation-coupled chromatin remodeling / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / transforming growth factor beta receptor signaling pathway / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / erythrocyte differentiation / PRC2 methylates histones and DNA / positive regulation of miRNA transcription / 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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / histone deacetylase binding / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||
Authors | Lian T / Guan R / Bai Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 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 | emd_28630.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-28630-v30.xml emd-28630.xml | 22.7 KB 22.7 KB | Display Display | EMDB header |
Images | emd_28630.png | 84.6 KB | ||
Filedesc metadata | emd-28630.cif.gz | 6.7 KB | ||
Others | emd_28630_half_map_1.map.gz emd_28630_half_map_2.map.gz | 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28630 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28630 | HTTPS FTP |
-Validation report
Summary document | emd_28630_validation.pdf.gz | 977.1 KB | Display | EMDB validaton report |
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Full document | emd_28630_full_validation.pdf.gz | 976.7 KB | Display | |
Data in XML | emd_28630_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_28630_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28630 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28630 | HTTPS FTP |
-Related structure data
Related structure data | 8eviMC 8evhC 8evjC 8sypC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28630.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_28630_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28630_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : nucleosome PU.1 mutant complex
+Supramolecule #1: nucleosome PU.1 mutant complex
+Macromolecule #1: DNA (167-MER)
+Macromolecule #2: DNA (167-MER)
+Macromolecule #3: Histone H3.1
+Macromolecule #4: Histone H4
+Macromolecule #5: Histone H2A type 2-C
+Macromolecule #6: Histone H2B type 2-E
+Macromolecule #7: Histone H2A type 2-C
+Macromolecule #8: Single-chain variable fragment
+Macromolecule #9: Transcription factor PU.1
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127327 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |