+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17740 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Nucleosome / nuclear receptor / NR5A2 / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of gene expression in early pancreatic precursor cells / G2/M DNA damage checkpoint / Recognition and association of DNA glycosylase with site containing an affected purine / HDMs demethylate histones / Cleavage of the damaged purine ...Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of gene expression in early pancreatic precursor cells / G2/M DNA damage checkpoint / Recognition and association of DNA glycosylase with site containing an affected purine / HDMs demethylate histones / Cleavage of the damaged purine / Nonhomologous End-Joining (NHEJ) / Condensation of Prophase Chromosomes / HDACs deacetylate histones / pancreas morphogenesis / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / HATs acetylate histones / calcineurin-mediated signaling / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / acinar cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / negative regulation of chromosome condensation / tissue development / Barr body / regulation of centromere complex assembly / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / bile acid metabolic process / embryo development ending in birth or egg hatching / oocyte maturation / oogenesis / homeostatic process / nucleus organization / chromosome, centromeric region / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / positive regulation of viral genome replication / CENP-A containing nucleosome / nucleosomal DNA binding / embryo implantation / hormone-mediated signaling pathway / innate immune response in mucosa / cellular response to leukemia inhibitory factor / transcription coregulator binding / cholesterol homeostasis / SUMOylation of intracellular receptors / multicellular organism growth / phospholipid binding / Nuclear Receptor transcription pathway / osteoblast differentiation / RNA polymerase II transcription regulator complex / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / nuclear receptor activity / male gonad development / nucleosome / sequence-specific double-stranded DNA binding / nucleosome assembly / chromatin organization / chromosome / regulation of cell population proliferation / antibacterial humoral response / positive regulation of cell growth / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / cell population proliferation / sequence-specific DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to Gram-positive bacterium / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.58 Å | |||||||||
Authors | Kobayashi W / Sappler A / Bollschweiler D / Kummecke M / Basquin J / Arslantas E / Ruangroengkulrith S / Hornberger R / Duderstadt K / Tachibana K | |||||||||
Funding support | Germany, European Union, 2 items
| |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition. Authors: Wataru Kobayashi / Anna H Sappler / Daniel Bollschweiler / Maximilian Kümmecke / Jérôme Basquin / Eda Nur Arslantas / Siwat Ruangroengkulrith / Renate Hornberger / Karl Duderstadt / Kikuë Tachibana / Abstract: Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed chromatin. Nr5a2 is a key pioneer factor that regulates ...Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed chromatin. Nr5a2 is a key pioneer factor that regulates zygotic genome activation in totipotent embryos, pluripotency in embryonic stem cells and metabolism in adult tissues, but the mechanism of its pioneer activity remains poorly understood. Here, we present a cryo-electron microscopy structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved carboxy-terminal extension (CTE) loop of the NR5A2 DNA-binding domain competes with a DNA minor groove anchor of the nucleosome and releases entry-exit site DNA. Mutational analysis showed that NR5A2 D159 of the CTE is dispensable for DNA binding but required for stable nucleosome association and persistent DNA 'unwrapping'. These findings suggest that NR5A2 belongs to an emerging class of pioneer factors that can use DNA minor groove anchor competition to destabilize nucleosomes and facilitate gene expression during reprogramming. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_17740.map.gz | 63 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-17740-v30.xml emd-17740.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17740_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_17740.png | 70.2 KB | ||
Filedesc metadata | emd-17740.cif.gz | 6.5 KB | ||
Others | emd_17740_half_map_1.map.gz emd_17740_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17740 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17740 | HTTPS FTP |
-Validation report
Summary document | emd_17740_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_17740_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17740_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_17740_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17740 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17740 | HTTPS FTP |
-Related structure data
Related structure data | 8pkiMC 8pkjC 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_17740.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.8512 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_17740_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_17740_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5
Entire | Name: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5 |
---|---|
Components |
|
-Supramolecule #1: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5
Supramolecule | Name: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Histone H3.3
Macromolecule | Name: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 15.360983 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.3 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
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 #3: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
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 |
-Macromolecule #4: Histone H2B type 1-C/E/G
Macromolecule | Name: Histone H2B type 1-C/E/G / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 13.937213 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK UniProtKB: Histone H2B type 1-C/E/G |
-Macromolecule #7: Nuclear receptor subfamily 5 group A member 2
Macromolecule | Name: Nuclear receptor subfamily 5 group A member 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.989939 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: LCPVCGDKVS GYHYGLLTCE SCKGFFKRTV QNNKRYTCIE NQNCQIDKTQ RKRCPYCRFQ KCLSVGMKLE AVRADRMRGG RNKFGPMYK RDRAL UniProtKB: Nuclear receptor subfamily 5 group A member 2 |
-Macromolecule #5: DNA
Macromolecule | Name: DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 46.968922 KDa |
Sequence | String: (DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG) (DT)(DA)(DG)(DA)(DC)(DA) ...String: (DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC) (DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG) (DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC) (DT)(DG)(DT) (DC)(DC)(DC)(DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC) (DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG)(DG) (DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT) (DA)(DG)(DT)(DC)(DT) (DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DT)(DC)(DA)(DA) (DG)(DG)(DC)(DC)(DA)(DA) (DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DA)(DT) |
-Macromolecule #6: DNA
Macromolecule | Name: DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 47.489234 KDa |
Sequence | String: (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DT)(DG)(DG)(DC)(DC)(DT) (DT)(DG)(DA)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA) ...String: (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DT)(DG)(DG)(DC)(DC)(DT) (DT)(DG)(DA)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG) (DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG) (DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG) (DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG) (DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DA)(DT) |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-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 | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |