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Yorodumi- EMDB-43195: Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43195 | |||||||||
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Title | Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) | |||||||||
Map data | ||||||||||
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 / mesenchymal-epithelial cell signaling involved in prostate gland development / anatomical structure formation involved in morphogenesis / positive regulation of cell-cell adhesion mediated by cadherin / epithelial cell maturation involved in prostate gland development / neuron fate specification / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development ...alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / mesenchymal-epithelial cell signaling involved in prostate gland development / anatomical structure formation involved in morphogenesis / positive regulation of cell-cell adhesion mediated by cadherin / epithelial cell maturation involved in prostate gland development / neuron fate specification / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / lung epithelial cell differentiation / dorsal/ventral neural tube patterning / prostate gland epithelium morphogenesis / dopaminergic neuron differentiation / Formation of axial mesoderm / hormone metabolic process / positive regulation of smoothened signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / smoothened signaling pathway / epithelial tube branching involved in lung morphogenesis / microvillus / negative regulation of tumor necrosis factor-mediated signaling pathway / anatomical structure morphogenesis / negative regulation of megakaryocyte differentiation / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Notch signaling pathway / 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 / Assembly of the ORC complex at the origin of replication / positive regulation of mitotic cell cycle / SUMOylation of chromatin organization proteins / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / positive regulation of DNA-binding transcription factor activity / 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 / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / fibrillar center / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / 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 / sequence-specific double-stranded DNA binding / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / antibacterial humoral response / glucose homeostasis / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / gene expression Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 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_43195.map.gz | 32.1 MB | EMDB map data format | |
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Header (meta data) | emd-43195-v30.xml emd-43195.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43195_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_43195.png | 99.8 KB | ||
Masks | emd_43195_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-43195.cif.gz | 6.8 KB | ||
Others | emd_43195_half_map_1.map.gz emd_43195_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43195 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43195 | HTTPS FTP |
-Validation report
Summary document | emd_43195_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_43195_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_43195_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_43195_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43195 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43195 | HTTPS FTP |
-Related structure data
Related structure data | 8vfzMC 8vfxC 8vfyC 8vg0C 8vg1C 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_43195.map.gz / Format: CCP4 / Size: 64 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: 1.32 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43195_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43195_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43195_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : FoxA1 in complx with 186bp ALBN1 nucleosome
Entire | Name: FoxA1 in complx with 186bp ALBN1 nucleosome |
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Components |
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-Supramolecule #1: FoxA1 in complx with 186bp ALBN1 nucleosome
Supramolecule | Name: FoxA1 in complx with 186bp ALBN1 nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Hepatocyte nuclear factor 3-alpha
Macromolecule | Name: Hepatocyte nuclear factor 3-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.022562 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLGTVKMEGH ETSDWNSYYA DTQEAYSSVP VSNMNSGLGS MNSMNTYMTM NTMTTSGNMT PASFNMSYAN PGLGAGLSPG AVAGMPGGS AGAMNSMTAA GVTAMGTALS PSGMGAMGAQ QAASMNGLGP YAAAMNPCMS PMAYAPSNLG RSRAGGGGDA K TFKRSYPH ...String: MLGTVKMEGH ETSDWNSYYA DTQEAYSSVP VSNMNSGLGS MNSMNTYMTM NTMTTSGNMT PASFNMSYAN PGLGAGLSPG AVAGMPGGS AGAMNSMTAA GVTAMGTALS PSGMGAMGAQ QAASMNGLGP YAAAMNPCMS PMAYAPSNLG RSRAGGGGDA K TFKRSYPH AKPPYSYISL ITMAIQQAPS KMLTLSEIYQ WIMDLFPYYR QNQQRWQNSI RHSLSFNDCF VKVARSPDKP GK GSYWTLH PDSGNMFENG CYLRRQKRFK CEKQPGAGGG GGSGSGGSGA KGGPESRKDP SGASNPSADS PLHRGVHGKT GQL EGAPAP GPAASPQTLD HSGATATGGA SELKTPASST APPISSGPGA LASVPASHPA HGLAPHESQL HLKGDPHYSF NHPF SINNL MSSSEQQHKL DFKAYEQALQ YSPYGSTLPA SLPLGSASVT TRSPIEPSAL EPAYYQGVYS RPVLNTSHHH HHH UniProtKB: Hepatocyte nuclear factor 3-alpha |
-Macromolecule #4: Histone H2A type 1-B/E
Macromolecule | Name: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.165551 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K UniProtKB: Histone H2A type 1-B/E |
-Macromolecule #5: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.437167 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.1 |
-Macromolecule #6: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #7: Histone H2B type 1-J
Macromolecule | Name: Histone H2B type 1-J / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.935239 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK UniProtKB: Histone H2B type 1-J |
-Macromolecule #2: DNA (171-MER)
Macromolecule | Name: DNA (171-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 57.399637 KDa |
Sequence | String: (DA)(DT)(DC)(DC)(DG)(DA)(DG)(DA)(DT)(DG) (DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DT)(DC)(DC)(DT)(DG)(DC)(DT) (DC)(DT)(DG)(DT)(DC)(DA)(DG)(DC)(DA)(DG) (DG) (DG)(DC)(DA)(DC)(DT)(DG) ...String: (DA)(DT)(DC)(DC)(DG)(DA)(DG)(DA)(DT)(DG) (DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DT)(DC)(DC)(DT)(DG)(DC)(DT) (DC)(DT)(DG)(DT)(DC)(DA)(DG)(DC)(DA)(DG) (DG) (DG)(DC)(DA)(DC)(DT)(DG)(DT)(DA) (DC)(DT)(DT)(DG)(DC)(DT)(DG)(DA)(DT)(DA) (DC)(DC) (DA)(DG)(DG)(DG)(DA)(DA)(DT) (DG)(DT)(DT)(DT)(DG)(DT)(DT)(DC)(DT)(DT) (DA)(DA)(DA) (DT)(DA)(DC)(DC)(DA)(DT) (DC)(DA)(DT)(DT)(DC)(DC)(DG)(DG)(DA)(DC) (DG)(DT)(DG)(DT) (DT)(DT)(DG)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DT)(DT) (DT)(DT)(DC)(DC)(DA) (DT)(DG)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DG)(DA)(DA)(DA) (DG)(DA)(DA)(DG)(DT)(DT) (DT)(DG)(DG) (DA)(DC)(DT)(DG)(DA)(DT)(DC)(DA)(DA)(DT) (DA)(DC)(DA)(DG)(DT)(DC)(DC) (DT)(DC) (DT)(DG)(DC)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DC)(DA)(DA)(DT)(DA)(DG)(DG) (DA) (DA)(DA)(DG)(DA)(DT) |
-Macromolecule #3: DNA (171-MER)
Macromolecule | Name: DNA (171-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 57.42777 KDa |
Sequence | String: (DA)(DT)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DA) (DT)(DT)(DG)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DG)(DC)(DA)(DG)(DA)(DG)(DG)(DA) (DC)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DT) (DC) (DA)(DG)(DT)(DC)(DC)(DA) ...String: (DA)(DT)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DA) (DT)(DT)(DG)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DG)(DC)(DA)(DG)(DA)(DG)(DG)(DA) (DC)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DT) (DC) (DA)(DG)(DT)(DC)(DC)(DA)(DA)(DA) (DC)(DT)(DT)(DC)(DT)(DT)(DT)(DC)(DT)(DG) (DC)(DA) (DT)(DG)(DT)(DA)(DC)(DA)(DT) (DG)(DG)(DA)(DA)(DA)(DA)(DC)(DT)(DG)(DG) (DC)(DC)(DA) (DA)(DG)(DG)(DC)(DA)(DA) (DA)(DC)(DA)(DC)(DG)(DT)(DC)(DC)(DG)(DG) (DA)(DA)(DT)(DG) (DA)(DT)(DG)(DG)(DT) (DA)(DT)(DT)(DT)(DA)(DA)(DG)(DA)(DA)(DC) (DA)(DA)(DA)(DC)(DA) (DT)(DT)(DC)(DC) (DC)(DT)(DG)(DG)(DT)(DA)(DT)(DC)(DA)(DG) (DC)(DA)(DA)(DG)(DT)(DA) (DC)(DA)(DG) (DT)(DG)(DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG) (DA)(DC)(DA)(DG)(DA)(DG)(DC) (DA)(DG) (DG)(DA)(DG)(DA)(DC)(DA)(DC)(DA)(DA)(DA) (DG)(DT)(DA)(DC)(DC)(DA)(DT)(DC) (DT) (DC)(DG)(DG)(DA)(DT) |
-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 |