+Open data
-Basic information
Entry | Database: PDB / ID: 8pki | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 | |||||||||
Components |
| |||||||||
Keywords | DNA BINDING PROTEIN / Nucleosome / nuclear receptor / NR5A2 | |||||||||
Function / homology | Function and homology information negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / SUMOylation of chromatin organization proteins / Deposition of new CENPA-containing nucleosomes at the centromere / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of gene expression in early pancreatic precursor cells / Condensation of Prophase Chromosomes / G2/M DNA damage checkpoint / HDMs demethylate histones ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / SUMOylation of chromatin organization proteins / Deposition of new CENPA-containing nucleosomes at the centromere / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of gene expression in early pancreatic precursor cells / Condensation of Prophase Chromosomes / G2/M DNA damage checkpoint / HDMs demethylate histones / Processing of DNA double-strand break ends / Nonhomologous End-Joining (NHEJ) / muscle cell differentiation / pancreas morphogenesis / PRC2 methylates histones and DNA / 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 / pericentric heterochromatin formation / inner kinetochore / acinar cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / tissue development / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / oocyte maturation / bile acid metabolic process / embryo development ending in birth or egg hatching / nucleosomal DNA binding / nucleus organization / oogenesis / homeostatic process / single fertilization / spermatid development / subtelomeric heterochromatin formation / chromosome, centromeric region / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / positive regulation of viral genome replication / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / embryo implantation / cellular response to leukemia inhibitory factor / hormone-mediated signaling pathway / response to hormone / cholesterol homeostasis / innate immune response in mucosa / transcription coregulator binding / phospholipid binding / multicellular organism growth / SUMOylation of intracellular receptors / osteoblast differentiation / nucleosome assembly / Nuclear Receptor transcription pathway / structural constituent of chromatin / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / sequence-specific double-stranded DNA binding / chromosome / chromatin organization / regulation of cell population proliferation / antibacterial humoral response / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / 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, 2items
| |||||||||
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
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8pki.cif.gz | 390.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8pki.ent.gz | 239.8 KB | Display | PDB format |
PDBx/mmJSON format | 8pki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/8pki ftp://data.pdbj.org/pub/pdb/validation_reports/pk/8pki | HTTPS FTP |
---|
-Related structure data
Related structure data | 17740MC 8pkjC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 5 types, 9 molecules AEBFCGDHK
#1: Protein | Mass: 15360.983 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H3-3a, H3.3a, H3f3a, H3-3b, H3.3b, H3f3b / Production host: Escherichia coli (E. coli) / References: UniProt: P84244 #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Gene: H4c1, Hist1h4a, H4c2, H4-53, Hist1h4b, H4c3, H4-12, Hist1h4c, H4c4, Hist1h4d, H4c6, Hist1h4f, H4c8, Hist1h4h, H4c9, Hist1h4i, H4c11, Hist1h4j, H4c12, Hist1h4k, Hist1h4m, H4c14, Hist2h4, ...Gene: H4c1, Hist1h4a, H4c2, H4-53, Hist1h4b, H4c3, H4-12, Hist1h4c, H4c4, Hist1h4d, H4c6, Hist1h4f, H4c8, Hist1h4h, H4c9, Hist1h4i, H4c11, Hist1h4j, H4c12, Hist1h4k, Hist1h4m, H4c14, Hist2h4, Hist2h4a, H4c16, H4f16, Hist4h4 Production host: Escherichia coli (E. coli) / References: UniProt: P62806 #3: Protein | Mass: 14165.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist1h2ad / Production host: Escherichia coli (E. coli) / References: UniProt: B2RVF0 #4: Protein | Mass: 13937.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2bc4, Hist1h2bc, H2bc6, Hist1h2be, H2bc8, Hist1h2bg / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZWY9 #7: Protein | | Mass: 10989.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Production host: Escherichia coli (E. coli) / References: UniProt: O00482 |
---|
-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 46968.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
---|---|
#6: DNA chain | Mass: 47489.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 1 types, 1 molecules
#8: Chemical | ChemComp-ZN / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5 Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 65.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 653440 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 110.27 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
|