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- PDB-7x3x: Cryo-EM structure of N1 nucleosome-RA -

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Basic information

Entry
Database: PDB / ID: 7x3x
TitleCryo-EM structure of N1 nucleosome-RA
Components
  • (DNA (146-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • ISWI chromatin-remodeling complex ATPase ISW1
KeywordsPROTEIN BINDING/DNA / PROTEIN BINDING-DNA COMPLEX
Function / homology
Function and homology information


Isw1b complex / Isw1a complex / Isw1 complex / regulation of transcriptional start site selection at RNA polymerase II promoter / nucleolar chromatin / 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 / regulation of transcriptional start site selection at RNA polymerase II promoter / nucleolar chromatin / 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 / mRNA 3'-UTR binding / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / 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 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 / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / 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 / 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
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B 1.1 / ISWI chromatin-remodeling complex ATPase ISW1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae S288C (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLifei, L. / Kangjing, C. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structure of the ISW1a complex bound to the dinucleosome.
Authors: Lifei Li / Kangjing Chen / Youyang Sia / Pengjing Hu / Youpi Ye / Zhucheng Chen /
Abstract: Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin ...Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment.
History
DepositionMar 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
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Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
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Revision 1.4Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (146-MER)
J: DNA (146-MER)
V: ISWI chromatin-remodeling complex ATPase ISW1


Theoretical massNumber of molelcules
Total (without water)323,53111
Polymers323,53111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules AEBFCGDHV

#1: Protein Histone H3


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h2ac14.L, h2ac14, hist1h2aj / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13965.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#7: Protein ISWI chromatin-remodeling complex ATPase ISW1


Mass: 123301.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: ISW1, YBR245C, YBR1633 / Production host: Escherichia coli (E. coli)
References: UniProt: P38144, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (146-MER)


Mass: 45154.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (146-MER)


Mass: 45265.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1IOC3-N2 nucleosomeCOMPLEXall0MULTIPLE SOURCES
2N2 nucleosomeCOMPLEX#1-#41RECOMBINANT
3DNACOMPLEX#5-#61SYNTHETIC
4IOC3COMPLEX#71RECOMBINANT
Molecular weightValue: 392 kDa/nm / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Xenopus laevis (African clawed frog)8355
23Saccharomyces cerevisiae S288C (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMsodium chlorideNaCl1
210 mMtrisTris1
32 mMmagnesium chlorideMgCl21
SpecimenConc.: 1 mg/ml / Embedding 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170126 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01212844
ELECTRON MICROSCOPYf_angle_d0.97218612
ELECTRON MICROSCOPYf_dihedral_angle_d31.8763789
ELECTRON MICROSCOPYf_chiral_restr0.0622128
ELECTRON MICROSCOPYf_plane_restr0.0061347

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