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Yorodumi- EMDB-42094: Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome ... -
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Basic information
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| Title | Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) | |||||||||
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Keywords | nucleosome / pioneer transcription factors / DNA binding proteins / transcription / NUCLEAR PROTEIN | |||||||||
| Function / homology | Function and homology informationnoradrenergic neuron fate commitment / spinal cord oligodendrocyte cell differentiation / spinal cord oligodendrocyte cell fate specification / oligodendrocyte cell fate commitment / commitment of neuronal cell to specific neuron type in forebrain / regulation of timing of subpallium neuron differentiation / lung neuroendocrine cell differentiation / stomach neuroendocrine cell differentiation / carotid body glomus cell differentiation / subpallium neuron fate commitment ...noradrenergic neuron fate commitment / spinal cord oligodendrocyte cell differentiation / spinal cord oligodendrocyte cell fate specification / oligodendrocyte cell fate commitment / commitment of neuronal cell to specific neuron type in forebrain / regulation of timing of subpallium neuron differentiation / lung neuroendocrine cell differentiation / stomach neuroendocrine cell differentiation / carotid body glomus cell differentiation / subpallium neuron fate commitment / cerebral cortex GABAergic interneuron differentiation / ventral spinal cord interneuron fate commitment / adrenal chromaffin cell differentiation / cellular response to magnetism / parasympathetic nervous system development / vitamin D response element binding / vestibular nucleus development / noradrenergic neuron development / olfactory pit development / musculoskeletal movement, spinal reflex action / spinal cord association neuron differentiation / forebrain neuron differentiation / neuroblast fate determination / regulation of epithelial cell differentiation / bHLH transcription factor binding / neuron fate specification / cell development / natural killer cell differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of Notch signaling pathway / sympathetic ganglion development / lymphocyte differentiation / neuron fate commitment / sensory organ development / immunoglobulin V(D)J recombination / Peyer's patch development / sympathetic nervous system development / Myogenesis / response to folic acid / enteric nervous system development / pattern specification process / glial cell differentiation / response to epidermal growth factor / oligodendrocyte development / positive regulation of neural precursor cell proliferation / mitogen-activated protein kinase kinase kinase binding / positive regulation of neurogenesis / negative regulation of neuron differentiation / generation of neurons / positive regulation of Notch signaling pathway / B cell lineage commitment / central nervous system neuron development / E-box binding / oligodendrocyte differentiation / regulation of G1/S transition of mitotic cell cycle / neuroblast proliferation / regulation of neurogenesis / response to retinoic acid / negative regulation of tumor necrosis factor-mediated signaling pathway / neuron development / cis-regulatory region sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Notch signaling pathway / positive regulation of B cell proliferation / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / cell maturation / positive regulation of cell cycle / Packaging Of Telomere Ends / gastrulation / positive regulation of neuron differentiation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / neurogenesis / regulation of mitotic cell cycle / epigenetic regulation of gene expression / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Interleukin-7 signaling / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Defective pyroptosis / innate immune response in mucosa Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Zhou BR / Bai Y | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2026Title: Distinct associations of pioneer factor Ascl1-E12a with nucleosomes drive changes in cell fate. Authors: Bing-Rui Zhou / Edgar Luzete-Monteiro / Jingchao Zhang / Naomi Takenaka / Hsin-Yao Tang / Meilin Fernandez Garcia / Mariel Coradin / Megan Frederick / Greg Donahue / Benjamin Garcia / Yawen ...Authors: Bing-Rui Zhou / Edgar Luzete-Monteiro / Jingchao Zhang / Naomi Takenaka / Hsin-Yao Tang / Meilin Fernandez Garcia / Mariel Coradin / Megan Frederick / Greg Donahue / Benjamin Garcia / Yawen Bai / Kenneth S Zaret / ![]() Abstract: Understanding how pioneer transcription factors target nucleosomal DNA and initiate chromatin accessibility reveals the earliest events in cell fate changes. We integrated structural, biochemical, ...Understanding how pioneer transcription factors target nucleosomal DNA and initiate chromatin accessibility reveals the earliest events in cell fate changes. We integrated structural, biochemical, and genomic approaches to assess how the pioneer factor Ascl1-E12a heterodimer perturbs nucleosomes in vitro and in vivo to induce a neural cell fate. Two Ascl1-E12a heterodimers shift and unwrap 15 bp of nucleosomal DNA in a stepwise manner while eliciting solvent exchanges within the octamer. Nucleosome binding, but not free DNA binding, by Ascl1-E12a is enhanced by two types of associations with the nucleosome that differentially affect the kinetics of DNA unwrapping and shifting. Nucleosome association mutants of Ascl1 perturb chromatin opening on linker histone-compacted nucleosome arrays-independent of nucleosome remodelers-and targeting of closed chromatin in vivo, with consequent deficiencies in cellular reprogramming. Our findings establish that distinct associations with nucleosomes are essential for the pioneer factor Ascl1 to overcome chromatin barriers to reprogram cell fate. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_42094.map.gz | 117.2 MB | EMDB map data format | |
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| Header (meta data) | emd-42094-v30.xml emd-42094.xml | 27.8 KB 27.8 KB | Display Display | EMDB header |
| Images | emd_42094.png | 110.2 KB | ||
| Filedesc metadata | emd-42094.cif.gz | 7.7 KB | ||
| Others | emd_42094_half_map_1.map.gz emd_42094_half_map_2.map.gz | 5.4 MB 5.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42094 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42094 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8ublMC ![]() 8u9sC ![]() 8ubiC ![]() 8ubjC ![]() 8ubkC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_42094.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| 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: #1
| File | emd_42094_half_map_1.map | ||||||||||||
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-Half map: #2
| File | emd_42094_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : 162bp NRCAM nucleosome in complex with Asc1/E12a
+Supramolecule #1: 162bp NRCAM nucleosome in complex with Asc1/E12a
+Macromolecule #1: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-B/E
+Macromolecule #4: Histone H2B type 1-J
+Macromolecule #7: scFv
+Macromolecule #8: Achaete-scute homolog 1
+Macromolecule #9: Transcription factor E2-alpha
+Macromolecule #5: NRCAM DNA (162-MER)
+Macromolecule #6: NRCAM DNA (162-MER)
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 1 items
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Processing
FIELD EMISSION GUN
