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- EMDB-28630: CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations -
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Open data
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Basic information
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Title | CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations | |||||||||
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![]() | nucleosome / transcription factor / transcription / chromatin binding protein-DNA complex / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | ![]() 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 / negative regulation of megakaryocyte differentiation / cis-regulatory region sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / lipopolysaccharide-mediated signaling pathway / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / protein sequestering activity / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / transforming growth factor beta receptor signaling pathway / DNA methylation / erythrocyte differentiation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / DNA-binding transcription repressor activity, RNA polymerase II-specific / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / histone deacetylase binding / positive regulation of miRNA transcription / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / antibacterial humoral response Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.64 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 | ![]() | 49.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.7 KB 22.7 KB | Display Display | ![]() |
Images | ![]() | 84.6 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() | 49 MB 49 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eviMC ![]() 8evhC ![]() 8evjC ![]() 8sypC 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_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 |
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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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![]() | 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: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127327 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |