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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 / Formation of lateral plate mesoderm ...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 / Formation of lateral plate mesoderm / anatomical structure formation involved in morphogenesis / 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 / cell growth involved in cardiac muscle cell development / atrial septum morphogenesis / cardiac muscle tissue regeneration / endocardial cushion development / neuron fate specification / Transcriptional regulation of testis differentiation / cardiac ventricle morphogenesis / Physiological factors / atrial septum primum morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / lung epithelial cell differentiation / embryonic foregut morphogenesis / atrioventricular canal development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dorsal/ventral neural tube patterning / endoderm development / Formation of definitive endoderm / prostate gland epithelium morphogenesis / Formation of axial mesoderm / dopaminergic neuron differentiation / positive regulation of BMP signaling pathway / positive regulation of smoothened signaling pathway / negative regulation of epithelial to mesenchymal transition / hormone metabolic process / response to vitamin A / regulation of cardiac muscle cell contraction / aortic valve morphogenesis / Cardiogenesis / positive regulation of intracellular estrogen receptor signaling pathway / ventricular septum development / negative regulation of cardiac muscle cell apoptotic process / DNA-binding transcription activator activity / smoothened signaling pathway / epithelial tube branching involved in lung morphogenesis / cell fate commitment / detection of maltose stimulus / maltose transport complex / NFAT protein binding / heart looping / carbohydrate transport / protein localization to CENP-A containing chromatin / microvillus / CENP-A containing nucleosome / negative regulation of apoptotic signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of vascular endothelial growth factor production / anatomical structure morphogenesis / 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 / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / response to mechanical stimulus / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / Notch signaling pathway / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / ATP-binding cassette (ABC) transporter complex / DNA methylation / positive regulation of mitotic cell cycle / negative regulation of autophagy 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: Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Authors: Zhou BR / Bai Y | |||||||||
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 | 23.1 KB 23.1 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 | 7.4 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 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 | ||||||||||||||||||||
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 |