[English] 日本語
Yorodumi- EMDB-43194: Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43194 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) | |||||||||
Map data | Main map | |||||||||
Sample |
| |||||||||
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 / Formation of axial mesoderm / dopaminergic neuron differentiation / positive regulation of smoothened signaling pathway / negative regulation of epithelial to mesenchymal transition / hormone metabolic process / positive regulation of intracellular estrogen receptor signaling pathway / smoothened signaling pathway / epithelial tube branching involved in lung morphogenesis / protein localization to CENP-A containing chromatin / microvillus / CENP-A containing nucleosome / negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / 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 / DNA methylation / positive regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / positive regulation of miRNA transcription / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of DNA-binding transcription factor activity / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / fibrillar center / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / sequence-specific double-stranded DNA binding / glucose homeostasis / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Authors | Zhou BR / Bai Y | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Mol.Cell / Year: 2024 Title: Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Authors: Zhou BR / Bai Y | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_43194.map.gz | 58.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-43194-v30.xml emd-43194.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
Images | emd_43194.png | 116 KB | ||
Filedesc metadata | emd-43194.cif.gz | 6.6 KB | ||
Others | emd_43194_half_map_1.map.gz emd_43194_half_map_2.map.gz | 2 MB 2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43194 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43194 | HTTPS FTP |
-Validation report
Summary document | emd_43194_validation.pdf.gz | 463.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_43194_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | emd_43194_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_43194_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43194 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43194 | HTTPS FTP |
-Related structure data
Related structure data | 8vfyMC 8vfzC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_43194.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_43194_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_43194_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : FoxA1 in complx with 186bp ALBN1 nucleosome
Entire | Name: FoxA1 in complx with 186bp ALBN1 nucleosome |
---|---|
Components |
|
-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 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
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 #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
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: Arachidonate 15-lipoxygenase |
-Macromolecule #3: Histone H2A type 1-B/E
Macromolecule | Name: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
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 #4: Histone H2B type 1-J
Macromolecule | Name: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
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 #7: Hepatocyte nuclear factor 3-alpha
Macromolecule | Name: Hepatocyte nuclear factor 3-alpha / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
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 #5: DNA (171-MER)
Macromolecule | Name: DNA (171-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
---|---|
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 #6: DNA (171-MER)
Macromolecule | Name: DNA (171-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
---|---|
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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
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 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 231331 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |