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- PDB-8pkj: Cryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5 -

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Basic information

Entry
Database: PDB / ID: 8pkj
TitleCryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5
Components
  • (DNA) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3 (Fragment)
  • Histone H4
KeywordsDNA BINDING PROTEIN / Nucleosome / nuclear receptor / NR5A2
Function / homology
Function and homology information


innate immune response in mucosa / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / antibacterial humoral response / nucleosome assembly / defense response to Gram-positive bacterium / protein heterodimerization activity / DNA binding / extracellular space ...innate immune response in mucosa / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / antibacterial humoral response / nucleosome assembly / defense response to Gram-positive bacterium / protein heterodimerization activity / DNA binding / extracellular space / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
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 H4, conserved site ...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 H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H4 / Histone H3 / Histone H2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsKobayashi, 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
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)ERC-CoG-818556 TotipotentZygotChromEuropean Union
CitationJournal: 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
DepositionJun 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3 (Fragment)
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3 (Fragment)
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA
J: DNA


Theoretical massNumber of molelcules
Total (without water)204,17510
Polymers204,17510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3 (Fragment)


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 Histone H4


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 Histone H2A


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 Histone H2B


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 DNA


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 DNA


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)

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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: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 65.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 473492 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 52.72 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004112494
ELECTRON MICROSCOPYf_angle_d0.586318138
ELECTRON MICROSCOPYf_chiral_restr0.03542074
ELECTRON MICROSCOPYf_plane_restr0.00451283
ELECTRON MICROSCOPYf_dihedral_angle_d31.2763736

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