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Yorodumi- PDB-8pkj: Cryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pkj | |||||||||
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Title | Cryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5 | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Nucleosome / nuclear receptor / NR5A2 | |||||||||
Function / homology | Function and homology information innate immune response in mucosa / structural constituent of chromatin / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-positive bacterium / protein heterodimerization activity / DNA binding / extracellular space / nucleoplasm ...innate immune response in mucosa / structural constituent of chromatin / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-positive bacterium / protein heterodimerization activity / DNA binding / extracellular space / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 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
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pkj.cif.gz | 376.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pkj.ent.gz | 231.9 KB | Display | PDB format |
PDBx/mmJSON format | 8pkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pkj_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8pkj_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8pkj_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 8pkj_validation.cif.gz | 62 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/8pkj ftp://data.pdbj.org/pub/pdb/validation_reports/pk/8pkj | HTTPS FTP |
-Related structure data
Related structure data | 17741MC 8pkiC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#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: SERLUN_R04475 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7L1D652 #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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q2Z0K7 #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: CR201_G0046179 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2J8S4Y0 |
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-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) |
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#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) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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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: all / Source: RECOMBINANT |
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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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / 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 | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 473492 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.72 Å2 | ||||||||||||||||||||||||
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