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- PDB-5x0y: Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the... -

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Basic information

Entry
Database: PDB / ID: 5x0y
TitleComplex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome
Components
  • (DNA (167-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Transcription regulatory protein SNF2
KeywordsSTRUCTURAL PROTEIN/HYDROLASE/DNA / Snf2 / nucleosome / chromatin remodeling / STRUCTURAL PROTEIN-HYDROLASE-DNA complex
Function / homologyHistone-fold / Helicase/SANT-associated domain / SNF2-related, N-terminal domain / Histone H2B / Bromodomain / Helicase, C-terminal / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 ...Histone-fold / Helicase/SANT-associated domain / SNF2-related, N-terminal domain / Histone H2B / Bromodomain / Helicase, C-terminal / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Helicase superfamily 1/2, ATP-binding domain / Glutamine-Leucine-Glutamine, QLQ / SNF2 family N-terminal domain / AT hook, DNA-binding motif / Bromodomain, conserved site / Histone H4, conserved site / P-loop containing nucleoside triphosphate hydrolase / Snf2, ATP coupling domain / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / Bromodomain-like superfamily / SNF2-like, N-terminal domain superfamily / Histone H3/CENP-A / Helicase conserved C-terminal domain / |Bromodomain / C-terminus of histone H2A / QLQ domain profile. / HSA domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Bromodomain profile. / Histone H3 signature 2. / Bromodomain signature. / Histone H2B signature. / Histone H3 signature 1. / Histone H4 signature. / Histone H2A signature. / Core histone H2A/H2B/H3/H4 / Centromere kinetochore component CENP-T histone fold / Snf2-ATP coupling, chromatin remodelling complex / |QLQ / |HSA / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation / cellular alcohol catabolic process / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / sucrose catabolic process / nucleosome mobilization / SWI/SNF complex / strand invasion / rDNA binding / ATP-dependent chromatin remodeling / ec:3.6.4.-: / DNA-dependent ATPase activity / RNA polymerase II activating transcription factor binding / nucleosomal DNA binding / DNA-templated transcription, initiation / lysine-acetylated histone binding / double-strand break repair / nucleosome / helicase activity / DNA-dependent DNA replication / nucleosome assembly / chromatin remodeling / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / transcription, DNA-templated / DNA binding / nucleoplasm / ATP binding / nucleus / Histone H2B 1.1 / Histone H2A type 1 / Transcription regulatory protein SNF2 / Histone H4 / Histone H3.2 / Histone H2A
Function and homology information
Specimen sourceXenopus laevis / African clawed frog / amphibia / African clawed frog /
Saccharomyces cerevisiae / Yeast / yeast /
Synthetic construct
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.69 Å resolution
AuthorsLi, M. / Liu, X. / Xia, X. / Chen, Z. / Li, X.
CitationJournal: Nature / Year: 2017
Title: Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure.
Authors: Xiaoyu Liu / Meijing Li / Xian Xia / Xueming Li / Zhucheng Chen
Abstract: Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron ...Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling. Snf2 binds to the phosphate backbones of one DNA gyre of the nucleosome mainly through its helicase motifs within the major domain cleft, suggesting a conserved mechanism of substrate engagement across different remodellers. Snf2 contacts the second DNA gyre via a positively charged surface, providing a mechanism to anchor the remodeller at a fixed position of the nucleosome. Snf2 locally deforms nucleosomal DNA at the site of binding, priming the substrate for the remodelling reaction. Together, these findings provide mechanistic insights into chromatin remodelling.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 23, 2017 / Release: Apr 19, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 19, 2017Structure modelrepositoryInitial release
1.1Apr 26, 2017Structure modelRefinement description
1.2Jun 7, 2017Structure modelDatabase references

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-6700
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (167-MER)
J: DNA (167-MER)
O: Transcription regulatory protein SNF2


Theoretical massNumber of molelcules
Total (without water)297,02111
Polyers297,02111
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)55670
ΔGint (kcal/M)-376
Surface area (Å2)100870
MethodPISA

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Components

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Protein/peptide , 5 types, 9 molecules AEBFCGDHO

#1: Protein/peptide Histone H3.2


Mass: 15289.904 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / Production host: Escherichia coli / References: UniProt:P84233
#2: Protein/peptide Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / Production host: Escherichia coli / References: UniProt:P62799
#3: Protein/peptide Histone H2A /


Mass: 13978.241 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli / References: UniProt:Q6AZJ8, UniProt:P06897*PLUS
#4: Protein/peptide Histone H2B 1.1 / H2B1.1


Mass: 13524.752 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / Production host: Escherichia coli / References: UniProt:P02281
#7: Protein/peptide Transcription regulatory protein SNF2 / ATP-dependent helicase SNF2 / Regulatory protein GAM1 / Regulatory protein SWI2 / SWI/SNF complex component SNF2 / Transcription factor TYE3


Mass: 85802.805 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 666-1400
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / Gene: SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C / Production host: Escherichia coli / References: UniProt:P22082, EC:3.6.4.-

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (167-MER)


Mass: 51381.758 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#6: DNA chain DNA (167-MER)


Mass: 51723.949 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

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Details

Sequence detailsAuthors state that the sample sequence of chain D/H is conformed by DNA sequencing and consistents ...Authors state that the sample sequence of chain D/H is conformed by DNA sequencing and consistents with the literature (PDB code 3MVD).

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SHL2 complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae / Strain: ATCC 204508 / S288c
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil holey carbon grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 5 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategory
1e2boxer.py2particle selection
2UCSFImage4image acquisition
4CTFFind3CTF correction
13Relion1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 90725 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01217683
ELECTRON MICROSCOPYf_angle_d1.10625116
ELECTRON MICROSCOPYf_dihedral_angle_d20.25612340
ELECTRON MICROSCOPYf_chiral_restr0.0532861
ELECTRON MICROSCOPYf_plane_restr0.0062171

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