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- PDB-8pki: Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 -

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Basic information

Entry
Database: PDB / ID: 8pki
TitleCryo-EM structure of NR5A2-nucleosome complex SHL+5.5
Components
  • (DNA) x 2
  • Histone H2A
  • Histone H2B type 1-C/E/G
  • Histone H3.3
  • Histone H4
  • Nuclear receptor subfamily 5 group A member 2
KeywordsDNA BINDING PROTEIN / Nucleosome / nuclear receptor / NR5A2
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 / oocyte maturation / embryo development ending in birth or egg hatching / homeostatic process / oogenesis / nucleus organization / chromosome, centromeric region / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of viral genome replication / protein localization to CENP-A containing chromatin / 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
Nuclear hormone receptor family 5 / 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 ...Nuclear hormone receptor family 5 / 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. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A / Nuclear receptor subfamily 5 group A member 2 / Histone H4 / Histone H3.3 / Histone H2B type 1-C/E/G
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 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

Downloads & links

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Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
C: Histone H2A
D: Histone H2B type 1-C/E/G
E: Histone H3.3
F: Histone H4
G: Histone H2A
H: Histone H2B type 1-C/E/G
I: DNA
J: DNA
K: Nuclear receptor subfamily 5 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,23012
Polymers215,16411
Non-polymers651
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 , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3.3


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 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)
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 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 type 1-C/E/G


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 Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


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

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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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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: #1-#7 / 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: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 653440 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 110.27 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003212725
ELECTRON MICROSCOPYf_angle_d0.541118369
ELECTRON MICROSCOPYf_chiral_restr0.03112090
ELECTRON MICROSCOPYf_plane_restr0.00381381
ELECTRON MICROSCOPYf_dihedral_angle_d30.48863667

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