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- PDB-8vg1: Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome -

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Entry
Database: PDB / ID: 8vg1
TitleCryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome
Components
  • (DNA (171-MER)) x 2
  • Hepatocyte nuclear factor 3-alpha
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
  • Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4
KeywordsNUCLEAR PROTEIN/DNA / 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 / positive regulation of dopaminergic neuron differentiation / atrial septum secundum morphogenesis / atrioventricular valve formation / embryonic heart tube anterior/posterior pattern specification / transdifferentiation / mesenchymal-epithelial cell signaling involved in prostate gland development / Formation of lateral plate mesoderm / anatomical structure formation involved in morphogenesis ...alveolar secondary septum development / respiratory basal cell differentiation / positive regulation of dopaminergic neuron differentiation / atrial septum secundum morphogenesis / atrioventricular valve formation / embryonic heart tube anterior/posterior pattern specification / transdifferentiation / mesenchymal-epithelial cell signaling involved in prostate gland development / Formation of lateral plate mesoderm / anatomical structure formation involved in morphogenesis / intestinal epithelial cell differentiation / prostate gland stromal morphogenesis / cardiac right ventricle morphogenesis / positive regulation of cell-cell adhesion mediated by cadherin / atrioventricular node development / co-SMAD binding / atrial septum morphogenesis / epithelial cell maturation involved in prostate gland development / cardiac muscle tissue regeneration / cell growth involved in cardiac muscle cell development / Transcriptional regulation of testis differentiation / cardiac ventricle morphogenesis / neuron fate specification / endocardial cushion development / Physiological factors / atrial septum primum morphogenesis / atrioventricular canal development / lung epithelial cell differentiation / embryonic foregut morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dorsal/ventral neural tube patterning / prostate gland epithelium morphogenesis / Formation of definitive endoderm / endoderm development / Formation of axial mesoderm / dopaminergic neuron differentiation / positive regulation of BMP signaling pathway / Developmental Lineage of Pancreatic Acinar Cells / positive regulation of smoothened signaling pathway / hormone metabolic process / response to vitamin A / regulation of cardiac muscle cell contraction / aortic valve morphogenesis / Cardiogenesis / negative regulation of cardiac muscle cell apoptotic process / negative regulation of epithelial to mesenchymal transition / ventricular septum development / smoothened signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / DNA-binding transcription activator activity / NFAT protein binding / heart looping / detection of maltose stimulus / epithelial tube branching involved in lung morphogenesis / maltose transport complex / microvillus / carbohydrate transport / positive regulation of vascular endothelial growth factor production / negative regulation of apoptotic signaling pathway / anatomical structure morphogenesis / carbohydrate transmembrane transporter activity / maltose binding / cell fate commitment / maltose transport / negative regulation of tumor necrosis factor-mediated signaling pathway / maltodextrin transmembrane transport / response to mechanical stimulus / positive regulation of DNA-binding transcription factor activity / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of megakaryocyte differentiation / 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 / Packaging Of Telomere Ends / Notch signaling pathway / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / positive regulation of mitotic cell cycle / ATP-binding cassette (ABC) transporter complex / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / negative regulation of autophagy / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression
Similarity search - Function
GATA-type transcription activator, N-terminal / Transcription factor GATA-4/5/6 / GATA-type transcription activator, N-terminal / Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Transcription factor GATA / Fork head domain conserved site1 ...GATA-type transcription activator, N-terminal / Transcription factor GATA-4/5/6 / GATA-type transcription activator, N-terminal / Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Transcription factor GATA / Fork head domain conserved site1 / GATA-type zinc finger domain. / Fork head domain signature 1. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, NHR/GATA-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Maltose/maltodextrin-binding periplasmic protein / Transcription factor GATA-4 / Hepatocyte nuclear factor 3-alpha / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsZhou, B.R. / Bai, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: 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
DepositionDec 22, 2023Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (171-MER)
J: DNA (171-MER)
O: Hepatocyte nuclear factor 3-alpha
T: Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,66013
Polymers362,59512
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 10 molecules AEBFCGDHOT

#1: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15437.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14165.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13935.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#7: Protein Hepatocyte nuclear factor 3-alpha / HNF-3-alpha / HNF-3A / Forkhead box protein A1 / Transcription factor 3A / TCF-3A


Mass: 50022.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXA1, HNF3A, TCF3A / Production host: Escherichia coli (E. coli) / References: UniProt: P55317
#8: Protein Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / GATA-binding factor 4


Mass: 87880.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: malE, b4034, JW3994, GATA4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P43694

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (171-MER)


Mass: 57399.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (171-MER)


Mass: 57427.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 1 types, 1 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FoxA1 and GATA4 in complx with 186bp ALBN1 nucleosome / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
8PHENIXmodel refinement
13cryoSPARC4.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 403489 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00515406
ELECTRON MICROSCOPYf_angle_d0.71622273
ELECTRON MICROSCOPYf_dihedral_angle_d30.2184480
ELECTRON MICROSCOPYf_chiral_restr0.0382508
ELECTRON MICROSCOPYf_plane_restr0.0051639

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