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- EMDB-17740: Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5 -

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Entry
Database: EMDB / ID: EMD-17740
TitleCryo-EM structure of NR5A2-nucleosome complex SHL+5.5
Map data
Sample
  • Complex: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B type 1-C/E/G
    • DNA: DNA
    • DNA: DNA
    • Protein or peptide: Nuclear receptor subfamily 5 group A member 2
  • Ligand: ZINC ION
KeywordsNucleosome / nuclear receptor / NR5A2 / DNA BINDING PROTEIN
Function / homology
Function and homology information


Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / DNA Damage/Telomere Stress Induced Senescence / morula formation / Regulation of gene expression in early pancreatic precursor cells ...Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / SUMOylation of chromatin organization proteins / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / DNA Damage/Telomere Stress Induced Senescence / morula formation / Regulation of gene expression in early pancreatic precursor cells / G2/M DNA damage checkpoint / primary ovarian follicle growth / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / pancreas morphogenesis / HDACs deacetylate histones / PRC2 methylates histones and DNA / Processing of DNA double-strand break ends / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / inner cell mass cell differentiation / tissue development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / acinar cell differentiation / RMTs methylate histone arginines / negative regulation of chromosome condensation / Sertoli cell development / positive regulation of T cell anergy / positive regulation of stem cell differentiation / Barr body / Factors involved in megakaryocyte development and platelet production / : / Estrogen-dependent gene expression / embryonic cleavage / inner kinetochore / bile acid metabolic process / pericentric heterochromatin formation / embryo development ending in birth or egg hatching / exocrine pancreas development / muscle cell differentiation / cartilage development / negative regulation of chondrocyte differentiation / oocyte maturation / nucleosomal DNA binding / oogenesis / homeostatic process / nucleus organization / calcineurin-mediated signaling / spermatid development / chromosome, centromeric region / somatic stem cell population maintenance / single fertilization / subtelomeric heterochromatin formation / positive regulation of viral genome replication / protein localization to CENP-A containing chromatin / RNA polymerase II core promoter sequence-specific DNA binding / CENP-A containing nucleosome / hormone-mediated signaling pathway / neurogenesis / positive regulation of T cell proliferation / embryo implantation / cholesterol homeostasis / transcription coregulator binding / cellular response to leukemia inhibitory factor / SUMOylation of intracellular receptors / phospholipid binding / positive regulation of T cell activation / Nuclear Receptor transcription pathway / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / multicellular organism growth / nuclear receptor activity / male gonad development / osteoblast differentiation / sequence-specific double-stranded DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of cell growth / spermatogenesis / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / cell population proliferation / transcription cis-regulatory region binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin binding
Similarity search - Function
Nuclear hormone receptor family 5 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A ...Nuclear hormone receptor family 5 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Nuclear hormone receptor / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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 H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
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) / Homo sapiens (human) / synthetic construct (others)
Methodsingle 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, 2 items
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, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17740.png

Downloads & links

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Map

FileDownload / File: emd_17740.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272.384 Å		0.85 Å/pix.
x 320 pix.
= 272.384 Å		0.85 Å/pix.
x 320 pix.
= 272.384 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.26511073 - 0.72919405
Average (Standard dev.)0.0014476858 (±0.019433187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17740_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17740_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5

EntireName: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5
Components
  • Complex: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B type 1-C/E/G
    • DNA: DNA
    • DNA: DNA
    • Protein or peptide: Nuclear receptor subfamily 5 group A member 2
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of the nucleosome containing NR5A2 motif at SHL+5.5

SupramoleculeName: 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)

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Macromolecule #1: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.360983 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B type 1-C/E/G

MacromoleculeName: 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 weightTheoretical: 13.937213 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

UniProtKB: Histone H2B type 1-C/E/G

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Macromolecule #7: Nuclear receptor subfamily 5 group A member 2

MacromoleculeName: 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 weightTheoretical: 10.989939 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LCPVCGDKVS GYHYGLLTCE SCKGFFKRTV QNNKRYTCIE NQNCQIDKTQ RKRCPYCRFQ KCLSVGMKLE AVRADRMRGG RNKFGPMYK RDRAL

UniProtKB: Nuclear receptor subfamily 5 group A member 2

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Macromolecule #5: DNA

MacromoleculeName: DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.968922 KDa
SequenceString: (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)

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Macromolecule #6: DNA

MacromoleculeName: DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.489234 KDa
SequenceString: (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)

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 653440
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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