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Yorodumi- EMDB-43197: Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43197 | |||||||||
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Title | Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | nucleosome / pioneer transcription factors / DNA binding proteins / transcription / chromatin / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / atrial septum secundum morphogenesis / atrioventricular valve formation / transdifferentiation / embryonic heart tube anterior/posterior pattern specification / mesenchymal-epithelial cell signaling involved in prostate gland development / anatomical structure formation involved in morphogenesis ...alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / atrial septum secundum morphogenesis / atrioventricular valve formation / transdifferentiation / embryonic heart tube anterior/posterior pattern specification / mesenchymal-epithelial cell signaling involved in prostate gland development / anatomical structure formation involved in morphogenesis / Formation of lateral plate mesoderm / positive regulation of cell-cell adhesion mediated by cadherin / intestinal epithelial cell differentiation / epithelial cell maturation involved in prostate gland development / cardiac right ventricle morphogenesis / atrioventricular node development / co-SMAD binding / atrial septum morphogenesis / cell growth involved in cardiac muscle cell development / endocardial cushion development / cardiac muscle tissue regeneration / Transcriptional regulation of testis differentiation / neuron fate specification / cardiac ventricle morphogenesis / Physiological factors / atrial septum primum morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / atrioventricular canal development / embryonic foregut morphogenesis / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dorsal/ventral neural tube patterning / Formation of definitive endoderm / endoderm development / prostate gland epithelium morphogenesis / dopaminergic neuron differentiation / Formation of axial mesoderm / positive regulation of BMP signaling pathway / hormone metabolic process / positive regulation of smoothened signaling pathway / response to vitamin A / regulation of cardiac muscle cell contraction / aortic valve morphogenesis / Cardiogenesis / ventricular septum development / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / negative regulation of cardiac muscle cell apoptotic process / DNA-binding transcription activator activity / smoothened signaling pathway / epithelial tube branching involved in lung morphogenesis / NFAT protein binding / detection of maltose stimulus / heart looping / maltose transport complex / carbohydrate transport / microvillus / maltose binding / negative regulation of apoptotic signaling pathway / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / positive regulation of vascular endothelial growth factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / anatomical structure morphogenesis / negative regulation of megakaryocyte differentiation / cell fate commitment / protein localization to CENP-A containing chromatin / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Packaging Of Telomere Ends / response to mechanical stimulus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Notch signaling pathway / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / negative regulation of autophagy / Assembly of the ORC complex at the origin of replication / positive regulation of mitotic cell cycle / SUMOylation of chromatin organization proteins / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / HCMV Late Events Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.48 Å | |||||||||
Authors | Zhou BR / Bai Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4. Authors: Bing-Rui Zhou / Hanqiao Feng / Furong Huang / Iris Zhu / Stephanie Portillo-Ledesma / Dan Shi / Kenneth S Zaret / Tamar Schlick / David Landsman / Qianben Wang / Yawen Bai / Abstract: Mouse FOXA1 and GATA4 are prototypes of pioneer factors, initiating liver cell development by binding to the N1 nucleosome in the enhancer of the ALB1 gene. Using cryoelectron microscopy (cryo-EM), ...Mouse FOXA1 and GATA4 are prototypes of pioneer factors, initiating liver cell development by binding to the N1 nucleosome in the enhancer of the ALB1 gene. Using cryoelectron microscopy (cryo-EM), we determined the structures of the free N1 nucleosome and its complexes with FOXA1 and GATA4, both individually and in combination. We found that the DNA-binding domains of FOXA1 and GATA4 mainly recognize the linker DNA and an internal site in the nucleosome, respectively, whereas their intrinsically disordered regions interact with the acidic patch on histone H2A-H2B. FOXA1 efficiently enhances GATA4 binding by repositioning the N1 nucleosome. In vivo DNA editing and bioinformatics analyses suggest that the co-binding mode of FOXA1 and GATA4 plays important roles in regulating genes involved in liver cell functions. Our results reveal the mechanism whereby FOXA1 and GATA4 cooperatively bind to the nucleosome through nucleosome repositioning, opening chromatin by bending linker DNA and obstructing nucleosome packing. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43197.map.gz | 96.5 MB | EMDB map data format | |
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Header (meta data) | emd-43197-v30.xml emd-43197.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43197_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_43197.png | 109.5 KB | ||
Filedesc metadata | emd-43197.cif.gz | 7.5 KB | ||
Others | emd_43197_half_map_1.map.gz emd_43197_half_map_2.map.gz | 3.7 MB 3.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43197 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43197 | HTTPS FTP |
-Validation report
Summary document | emd_43197_validation.pdf.gz | 495.3 KB | Display | EMDB validaton report |
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Full document | emd_43197_full_validation.pdf.gz | 494.9 KB | Display | |
Data in XML | emd_43197_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_43197_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43197 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43197 | HTTPS FTP |
-Related structure data
Related structure data | 8vg1MC 8vfxC 8vfyC 8vfzC 8vg0C 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_43197.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||||||||||||||||||
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: half B
File | emd_43197_half_map_1.map | ||||||||||||
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Annotation | half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half A
File | emd_43197_half_map_2.map | ||||||||||||
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Annotation | half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : FoxA1 and GATA4 in complx with 186bp ALBN1 nucleosome
+Supramolecule #1: FoxA1 and GATA4 in complx with 186bp ALBN1 nucleosome
+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: Hepatocyte nuclear factor 3-alpha
+Macromolecule #8: Maltose/maltodextrin-binding periplasmic protein,Transcription fa...
+Macromolecule #5: DNA (171-MER)
+Macromolecule #6: DNA (171-MER)
+Macromolecule #9: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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 |