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

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Basic information

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 / 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
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 / Fork head domain signature 1. / GATA-type zinc finger domain. / 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. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Bacterial extracellular solute-binding protein / Lipoxygenase iron-binding catalytic domain profile. / Bacterial extracellular solute-binding protein / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / 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 / Arachidonate 15-lipoxygenase / 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: Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome
Authors: Zhou, B.R. / Bai, Y.
History
DepositionDec 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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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

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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 softwareName: cryoSPARC / Version: 4.1 / Category: 3D 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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