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- EMDB-63131: Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state -

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Entry
Database: EMDB / ID: EMD-63131
TitleStructure of isw1-nucleosome double-bound complex in ADP-ADP+ state
Map data
Sample
  • Complex: Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: ISWI chromatin-remodeling complex ATPase ISW1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsChromatin Remodeler / Nucleosome / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Isw1b complex / Isw1a complex / Isw1 complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of RNA export from nucleus / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding ...Isw1b complex / Isw1a complex / Isw1 complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of RNA export from nucleus / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding / nucleosome array spacer activity / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / nucleosome binding / helicase activity / mRNA 3'-UTR binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / heterochromatin formation / structural constituent of chromatin / nucleosome / response to heat / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Similarity search - Function
Isw1/2, N-terminal / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / : / SNF2-like, N-terminal domain superfamily ...Isw1/2, N-terminal / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / : / 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 H2A / Histone 2A / 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 / Helicase conserved C-terminal domain / Histone H3 signature 1. / Homeobox-like domain superfamily / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3 / Histone H2B / ISWI chromatin-remodeling complex ATPase ISW1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae S288C (yeast) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsSia Y / Pan H / Chen Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2025
Title: Structural insights into chromatin remodeling by ISWI during active ATP hydrolysis.
Authors: Youyang Sia / Han Pan / Kangjing Chen / Zhucheng Chen /
Abstract: Chromatin remodelers utilize the energy of adenosine triphosphate (ATP) hydrolysis to slide nucleosomes, regulating chromatin structure and gene activity in cells. In this work, we report structures ...Chromatin remodelers utilize the energy of adenosine triphosphate (ATP) hydrolysis to slide nucleosomes, regulating chromatin structure and gene activity in cells. In this work, we report structures of imitation switch (ISWI) bound to the nucleosome during active ATP hydrolysis and remodeling, revealing conformational transitions of the remodeling motor across the adenosine triphosphatase (ATPase) cycle. The DNA strands are distorted accordingly, showing one full base-pair bulge and a loss of histone contact at the site of motor binding in the adenosine diphosphate* b and Apo* states. We also identify several important elements for regulation of the remodeling activity. Notably, an enzyme conformation exiting the remodeling cycle reveals a linker DNA-sensing brake mechanism. Together, our findings elucidate a multistate model of ISWI action, providing a comprehensive mechanism of DNA translocation and regulation underpinning chromatin remodeling.
History
DepositionJan 14, 2025-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63131.png

Downloads & links

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Map

FileDownload / File: emd_63131.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 346.4 Å		1.08 Å/pix.
x 320 pix.
= 346.4 Å		1.08 Å/pix.
x 320 pix.
= 346.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.14051291 - 0.35203913
Average (Standard dev.)0.00011313938 (±0.008925467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63131_msk_1.map
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Half map: #2

Fileemd_63131_half_map_1.map
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Half map: #1

Fileemd_63131_half_map_2.map
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Sample components

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Entire : Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state

EntireName: Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state
Components
  • Complex: Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: ISWI chromatin-remodeling complex ATPase ISW1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state

SupramoleculeName: Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.560538 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAS EAYLVALFED TNLCAIHAKR VTIMPKDIQ LARRIRGER

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: 10.061849 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKRHRKVLRD NIQGITKPAI RRLARRGGVK RISGLIYEET RGVLKVFLEN VIRDAVTYTE HAKRKTVTAM DVVYALKRQG RTLYGFGG

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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.69465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKAKTRSSRA GLQFPVGRVH RLLRKGNYAE RVGAGAPVYL AAVLEYLTAE ILELAGNAAR DNKKTRIIPR HLQLAVRNDE ELNKLLGRV TIAQGGVLPN IQSVLLPK

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.348852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRKESYAIYV YKVLKQVHPD TGISSKAMSI MNSFVNDVFE RIAGEASRLA HYNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTK YTSA

UniProtKB: Histone H2B

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Macromolecule #7: ISWI chromatin-remodeling complex ATPase ISW1

MacromoleculeName: ISWI chromatin-remodeling complex ATPase ISW1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 131.303891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAYMLAIANF HFFKFYTRMR KKHENNSCNE KDKDENLFKI ILAIFLQEKK KYDCISSGSI MTASEEYLEN LKPFQVGLPP HDPESNKKR YLLKDANGKK FDLEGTTKRF EHLLSLSGLF KHFIESKAAK DPKFRQVLDV LEENKANGKG KGKHQDVRRR K TEHEEDAE ...String:
MAYMLAIANF HFFKFYTRMR KKHENNSCNE KDKDENLFKI ILAIFLQEKK KYDCISSGSI MTASEEYLEN LKPFQVGLPP HDPESNKKR YLLKDANGKK FDLEGTTKRF EHLLSLSGLF KHFIESKAAK DPKFRQVLDV LEENKANGKG KGKHQDVRRR K TEHEEDAE LLKEEDSDDD ESIEFQFRES PAYVNGQLRP YQIQGVNWLV SLHKNKIAGI LADEMGLGKT LQTISFLGYL RY IEKIPGP FLVIAPKSTL NNWLREINRW TPDVNAFILQ GDKEERAELI QKKLLGCDFD VVIASYEIII REKSPLKKIN WEY IIIDEA HRIKNEESML SQVLREFTSR NRLLITGTPL QNNLHELWAL LNFLLPDIFS DAQDFDDWFS SESTEEDQDK IVKQ LHTVL QPFLLRRIKS DVETSLLPKK ELNLYVGMSS MQKKWYKKIL EKDLDAVNGS NGSKESKTRL LNIMMQLRKC CNHPY LFDG AEPGPPYTTD EHLVYNAAKL QVLDKLLKKL KEEGSRVLIF SQMSRLLDIL EDYCYFRNYE YCRIDGSTAH EDRIQA IDD YNAPDSKKFV FLLTTRAGGL GINLTSADVV VLYDSDWNPQ ADLQAMDRAH RIGQKKQVKV FRLVTDNSVE EKILERA TQ KLRLDQLVIQ QNRTSLKKKE NKADSKDALL SMIQHGAADV FKSGTSTGSA GTPEPGSGEK GDDIDLDELL LKSENKTK S LNAKYETLGL DDLQKFNQDS AYEWNGQDFK KKIQRDIISP LLLNPTKRER KENYSIDNYY KDVLNTGRSS TPSHPRMPK PHVFHSHQLQ PPQLKVLYEK ERMWTAKKTG YVPTMDDVKA AYGDISDEEE KKQKLELLKL SVNNSQPLTE EEEKMKADWE SEGFTNWNK LEFRKFITVS GKYGRNSIQA IARELAPGKT LEEVRAYAKA FWSNIERIED YEKYLKIIEN EEEKIKRVKM Q QEALRRKL SEYKNPFFDL KLKHPPSSNN KRTYSEEEDR FILLMLFKYG LDRDDVYELV RDEIRDCPLF ELDFYFRSRT PV ELARRGN TLLQCLEKEF NAGIVLDDAT KDRMKKEDEN GKRIREEFAD QTANEKENVD GVESKKAKIE DTSNVGTEQL VAE KIPENE TTH

UniProtKB: ISWI chromatin-remodeling complex ATPase ISW1

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Macromolecule #5: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 45.222836 KDa
SequenceString: (DT)(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) ...String:
(DT)(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)(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)(DG)(DA)(DT)

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 45.521031 KDa
SequenceString: (DT)(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) ...String:
(DT)(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)(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)(DG)(DA)(DT)

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154464
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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