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- PDB-6k1p: The complex of ISWI-nucleosome in the ADP.BeF-bound state -

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Entry
Database: PDB / ID: 6k1p
TitleThe 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 / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Isw1a complex / Isw1b complex / heterochromatin maintenance involved in chromatin silencing / negative regulation of histone exchange / nucleolar chromatin / regulation of chromatin organization / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of nucleosome density / DNA-templated transcription, elongation / rDNA binding ...Isw1a complex / Isw1b complex / heterochromatin maintenance involved in chromatin silencing / negative regulation of histone exchange / nucleolar chromatin / regulation of chromatin organization / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of nucleosome density / DNA-templated transcription, elongation / rDNA binding / nucleosome binding / termination of RNA polymerase I transcription / ATP-dependent chromatin remodeling / sister chromatid cohesion / ec:3.6.4.-: / termination of RNA polymerase II transcription / DNA-templated transcription, initiation / helicase activity / nucleosome / transcription regulatory region DNA binding / chromatin remodeling / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Histone H2A/H2B/H3 / ISWI, HAND domain / Histone H2B / SANT/Myb domain / Helicase, C-terminal / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Homeobox-like domain superfamily / Histone-fold ...Histone H2A/H2B/H3 / ISWI, HAND domain / Histone H2B / SANT/Myb domain / Helicase, C-terminal / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Homeobox-like domain superfamily / Histone-fold / Helicase superfamily 1/2, ATP-binding domain / SLIDE domain / Histone H3/CENP-A / SANT domain / Histone H4, conserved site / P-loop containing nucleoside triphosphate hydrolase / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / ISWI, HAND domain superfamily / SNF2-like, N-terminal domain superfamily / Core histone H2A/H2B/H3/H4 / SNF2 family N-terminal domain / SNF2-related, N-terminal domain / Helicase conserved C-terminal domain / HAND / Histone H4 signature. / Histone H2B signature. / Histone H2A signature. / Histone H3 signature 2. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Histone H3 signature 1. / Superfamilies 1 and 2 helicase C-terminal domain profile. / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / SLIDE / SANT domain profile.
Histone H3 / Histone H2B 1.1 / ISWI chromatin-remodeling complex ATPase ISW1 / Histone H4 / Histone H2A
Biological speciesXenopus laevis (African clawed frog)
Escherichia coli K-12 (bacteria)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 10, 2019 / Release: May 29, 2019
RevisionDateData content typeProviderType
1.0May 29, 2019Structure modelrepositoryInitial release

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Structure visualization

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  • EMDB-9719
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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
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area59960 Å2
ΔGint-434 kcal/mol
Surface area97880 Å2

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Components

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Protein/peptide , 5 types, 9 molecules AEBFCGDHK

#1: Protein/peptide 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/peptide 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/peptide 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/peptide 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/peptide 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, EC: 3.6.4.-

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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-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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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

Source: RECOMBINANT / Type: COMPLEX

IDNameEntity IDParent-ID
1The complex of ISWI-nucleosome in the ADP.BeF-bound state1,2,3,4,5,6,70
2ISWIImitation SWI71
3nuleosome1,2,3,41
4DNA5,61
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
33Xenopus laevis (African clawed frog)8355
44Escherichia coli K-12 (bacteria)83333
Source (recombinant)

Ncbi tax-ID: 83333 / Organism: Escherichia coli K-12 (bacteria)

IDEntity assembly-ID
12
23
24
Buffer solutionpH: 8.5 / Details: 10 mM Tris, 50 mM NaCl
Buffer componentConc.: 1.35 mg/ml / Name: sodium chloride / Formula: NaClSodium chloride
SpecimenConc.: 0.1 mg/ml / Details: monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: no special treatment / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K / Details: blot for 1.5s

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Electron microscopy imaging

MicroscopyModel: FEI TITAN / Details: performed manually
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal magnification: 5000 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 µns / Alignment procedure: BASIC
Specimen holderCryogen: HELIUM
Model: GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Temperature (max): 100 K / Temperature (min): 100 K
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN29.03particle selection
2EMAN29.03image acquisition
4RELION3CTF correction
7UCSF Chimera1model fitting
9RELION3other
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13PHENIX13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62121 / Algorithm: FOURIER SPACE / Details: relion / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingB value: 200 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 5X0Y
Pdb chain-ID: A / Details: chimera / Pdb chain residue range: 1-1000

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