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- PDB-6jyl: The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state -

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Basic information

Entry
Database: PDB / ID: 6jyl
TitleThe crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state
Components
  • (DNA (167-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • ISWI chromatin-remodeling complex ATPase ISW1
KeywordsDNA BINDING PROTEIN/DNA / chromatin remodelling / single particle Cryo-EM / nucleosome / 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 / Histone, subunit A / Histone, subunit A ...Isw1/2, N-terminal / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / SANT domain profile. / SANT domain / Histone, subunit A / Histone, subunit A / : / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / 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)
Escherichia coli K-12 (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsYan, L.J. / Wu, H. / Li, X.M. / Gao, N. / Chen, Z.C.
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling.
Authors: Lijuan Yan / Hao Wu / Xuemei Li / Ning Gao / Zhucheng Chen /
Abstract: Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) ...Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) structures of Saccharomyces cerevisiae ISWI (ISW1) in complex with the nucleosome in adenosine diphosphate (ADP)-bound and ADP-BeF-bound states. The data show that after nucleosome binding, ISW1 is activated by substantial rearrangement of the catalytic domains, with the regulatory AutoN domain packing the first RecA-like core and the NegC domain being disordered. The high-resolution structure reveals local DNA distortion and translocation induced by ISW1 in the ADP-bound state, which is essentially identical to that induced by the Snf2 chromatin remodeler, suggesting a common mechanism of DNA translocation. The histone core remains largely unperturbed, and prevention of histone distortion by crosslinking did not inhibit the activity of yeast ISW1 or its human homolog. Together, our findings suggest a general mechanism of chromatin remodeling involving local DNA distortion without notable histone deformation.
History
DepositionApr 26, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 29, 2019ID: 6IRM
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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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 (167-MER)
J: DNA (167-MER)
K: ISWI chromatin-remodeling complex ATPase ISW1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,93514
Polymers334,41811
Non-polymers5183
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area59740 Å2
ΔGint-442 kcal/mol
Surface area98440 Å2

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3


Mass: 15303.930 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 K-12 (bacteria) / References: UniProt: A0A310TTQ1
#2: Protein Histone H4


Mass: 11263.231 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 K-12 (bacteria) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 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 K-12 (bacteria) / References: UniProt: P02281
#7: Protein ISWI chromatin-remodeling complex ATPase ISW1


Mass: 123170.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ISW1, YBR245C, YBR1633 / Production host: Escherichia coli K-12 (bacteria)
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 (167-MER)


Mass: 51357.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria)
#6: DNA chain DNA (167-MER)


Mass: 51748.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria)

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Non-polymers , 3 types, 3 molecules

#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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
1The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound stateCOMPLEX#1-#70RECOMBINANT
2ISWICOMPLEX#71RECOMBINANT
3nucleosomeCOMPLEX#1-#41RECOMBINANT
4DNACOMPLEX#5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
23Xenopus laevis (African clawed frog)8355
34Escherichia coli K-12 (bacteria)83333
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli K-12 (bacteria)83333
23Escherichia coli K-12 (bacteria)83333
34Escherichia coli K-12 (bacteria)83333
Buffer solutionpH: 8.5
Buffer componentConc.: 1.0 mg/ml / Name: sodium chloride / Formula: NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: blot 1.5s

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal magnification: 130000 X / Calibrated magnification: 29000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER
Temperature (max): 80 K / Temperature (min): 70 K / Residual tilt: 0.1 mradians
Image recordingAverage exposure time: 12 sec. / Electron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 5000
EM imaging opticsEnergyfilter name: GIF 2000 / Energyfilter slit width: 20 eV
Image scansSampling size: 10 µm / Width: 1034 / Height: 1034 / Movie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2SerialEM1image acquisition
4RELION3CTF correction
8PHENIX1model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 316230 / Algorithm: FOURIER SPACE / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingB value: 200 / Space: REAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 5X0Y

5x0y


Pdb chain-ID: A / Accession code: 5X0Y / Pdb chain residue range: 1-1000 / Source name: PDB / Type: experimental model

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