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- EMDB-45404: DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-45404
TitleDeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome
Map dataDeltaArp8 INO80 in complex with S.c. 0/40 Nucleosome, nucleosome, fullmap
Sample
  • Complex: DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome
    • Complex: Histone proteins
      • Complex: Histone proteins H2A, H2B, and H3
        • Protein or peptide: Histone H3
        • Protein or peptide: Histone H2A.1
        • Protein or peptide: Histone H2B.1
      • Complex: Histone H4
        • Protein or peptide: Histone H4
    • Complex: DNA
      • DNA: DNA (227-MER)
      • DNA: DNA (227-MER)
KeywordsChromatin Remodeler / nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones ...sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / DNA damage tolerance / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / intracellular copper ion homeostasis / Ub-specific processing proteases / CENP-A containing nucleosome / aerobic respiration / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
: / 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 ...: / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B.1 / Histone H2A.1 / Histone H3 / Histone H4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsWu H / Kaur U / Narlikar GJ / Cheng YF
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Science / Year: 2025
Title: Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning.
Authors: Upneet Kaur / Hao Wu / Yifan Cheng / Geeta J Narlikar /
Abstract: Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like ...Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180° away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.
History
DepositionJun 17, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45404.png

Downloads & links

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Map

FileDownload / File: emd_45404.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeltaArp8 INO80 in complex with S.c. 0/40 Nucleosome, nucleosome, fullmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 448 pix.
= 366.867 Å		0.82 Å/pix.
x 448 pix.
= 366.867 Å		0.82 Å/pix.
x 448 pix.
= 366.867 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8189 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0033
Minimum - Maximum-0.01379761 - 0.027472248
Average (Standard dev.)0.00005359474 (±0.0008014287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 366.8672 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeltaArp8 INO80 in complex with S.c. 0/40 Nucleosome,...

Fileemd_45404_additional_1.map
AnnotationDeltaArp8 INO80 in complex with S.c. 0/40 Nucleosome, INO80 Core Module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DeltaArp8 INO80 in complex with S.c. 0/40 Nucleosome,...

Fileemd_45404_half_map_1.map
AnnotationDeltaArp8 INO80 in complex with S.c. 0/40 Nucleosome, nucleosome, halfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DeltaArp8 INO80 in complex with S.c. 0/40 Nucleosome,...

Fileemd_45404_half_map_2.map
AnnotationDeltaArp8 INO80 in complex with S.c. 0/40 Nucleosome, nucleosome, halfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome

EntireName: DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome
Components
  • Complex: DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome
    • Complex: Histone proteins
      • Complex: Histone proteins H2A, H2B, and H3
        • Protein or peptide: Histone H3
        • Protein or peptide: Histone H2A.1
        • Protein or peptide: Histone H2B.1
      • Complex: Histone H4
        • Protein or peptide: Histone H4
    • Complex: DNA
      • DNA: DNA (227-MER)
      • DNA: DNA (227-MER)

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Supramolecule #1: DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome

SupramoleculeName: DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Histone proteins

SupramoleculeName: Histone proteins / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4

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Supramolecule #3: Histone proteins H2A, H2B, and H3

SupramoleculeName: Histone proteins H2A, H2B, and H3 / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #1, #3-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #4: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #5: DNA

SupramoleculeName: DNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 15.391007 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR EIRRFQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA IGALQESVEA YLVSLFEDTN LAAIHAKRVT IQKKDIKLAR RLRGERS

UniProtKB: Histone H3

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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: Xenopus laevis (African clawed frog)
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.1

MacromoleculeName: Histone H2A.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.013177 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAI RNDDELNKLL GNVTIAQGGV LPNIHQNLLP KKSAKATKAS QEL

UniProtKB: Histone H2A.1

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Macromolecule #4: Histone H2B.1

MacromoleculeName: Histone H2B.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.280362 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSAKAEKKPA SKAPAEKKPA AKKTSTSTDG KKRSKARKET YSSYIYKVLK QTHPDTGISQ KSMSILNSFV NDIFERIATE ASKLAAYNK KSTISAREIQ TAVRLILPGE LAKHAVSEGT RAVTKYSSST QA

UniProtKB: Histone H2B.1

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Macromolecule #5: DNA (227-MER)

MacromoleculeName: DNA (227-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 70.34775 KDa
SequenceString: (DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG) (DG)(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA) (DG)(DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA) (DC) (DT)(DA)(DT)(DC)(DC)(DG) ...String:
(DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG) (DG)(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA) (DG)(DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA) (DC) (DT)(DA)(DT)(DC)(DC)(DG)(DA)(DC) (DT)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DC) (DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT) (DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA)(DC)(DA) (DT)(DG)(DC) (DA)(DC)(DA)(DG)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC) (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)

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Macromolecule #6: DNA (227-MER)

MacromoleculeName: DNA (227-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 69.840398 KDa
SequenceString: (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) ...String:
(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)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG) (DC)(DG)(DA)(DC)(DC)(DT)(DT)(DG)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DA)(DG) (DT) (DC)(DG)(DG)(DA)(DT)(DA)(DG)(DT)(DG)(DT) (DT)(DC)(DC)(DG)(DA)(DG)(DC)(DT)(DC) (DC)(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DG)(DA) (DG)(DG)(DA)(DT)(DC)(DC)(DC)(DC)(DG)(DG) (DG)(DT)(DA)(DC)(DC)(DG)(DA)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36091
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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