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- PDB-5z3u: Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state -

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Entry
Database: PDB / ID: 5z3u
TitleStructure of Snf2-nucleosome complex at shl2 in ADP BeFx state
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 / complex / nucleosome / chromatin remodeling / gene regulation / STRUCTURAL PROTEIN-HYDROLASE-DNA complex
Function / homology
Function and homology information


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 invasive growth in response to glucose limitation / positive regulation of mating type switching / sucrose catabolic process / nucleosome mobilization / strand invasion / SWI/SNF complex / rDNA binding ...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 invasive growth in response to glucose limitation / positive regulation of mating type switching / sucrose catabolic process / nucleosome mobilization / strand invasion / SWI/SNF complex / 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 / helicase activity / nucleosome / double-strand break repair / DNA-dependent DNA replication / chromatin remodeling / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Helicase superfamily 1/2, ATP-binding domain / Glutamine-Leucine-Glutamine, QLQ / 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-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 / AT hook, DNA-binding motif / Bromodomain / 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 / Core histone H2A/H2B/H3/H4 / SNF2 family N-terminal domain / Histone H3/CENP-A / Helicase conserved C-terminal domain / C-terminus of histone H2A / Histone H3 signature 1. / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / 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. / Centromere kinetochore component CENP-T histone fold / Bromodomain signature. / Histone H2B signature. / HSA / Histone H2A signature. / Histone H4 signature.
Histone H2B 1.1 / Transcription regulatory protein SNF2 / Histone H4 / Histone H3.2 / Histone H2A
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Xenopus laevis (African clawed frog)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsLi, M. / Xia, X. / Liu, X. / Li, X. / Chen, Z.
CitationJournal: Nature / Year: 2019
Title: Mechanism of DNA translocation underlying chromatin remodelling by Snf2.
Authors: Meijing Li / Xian Xia / Yuanyuan Tian / Qi Jia / Xiaoyu Liu / Ying Lu / Ming Li / Xueming Li / Zhucheng Chen /
Abstract: Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme. Among the remodelling enzymes, Snf2 serves as the ...Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme. Among the remodelling enzymes, Snf2 serves as the prototype to study the action of this protein family. Snf2 and related enzymes share two conserved RecA-like lobes, which by themselves are able to couple ATP hydrolysis to chromatin remodelling. The mechanism by which these enzymes couple ATP hydrolysis to translocate the nucleosome along the DNA remains unclear. Here we report the structures of Saccharomyces cerevisiae Snf2 bound to the nucleosome in the presence of ADP and ADP-BeF. Snf2 in the ADP-bound state adopts an open conformation similar to that in the apo state, and induces a one-base-pair DNA bulge at superhelix location 2 (SHL2), with the tracking strand showing greater distortion than the guide strand. The DNA distortion propagates to the proximal end, leading to staggered translocation of the two strands. The binding of ADP-BeF triggers a closed conformation of the enzyme, resetting the nucleosome to a relaxed state. Snf2 shows altered interactions with the DNA in different nucleotide states, providing the structural basis for DNA translocation. Together, our findings suggest a fundamental mechanism for the DNA translocation that underlies chromatin remodelling.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 8, 2018 / Release: May 22, 2019
RevisionDateData content typeProviderType
1.0May 22, 2019Structure modelrepositoryInitial release

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Structure visualization

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Assembly

Deposited unit
O: Transcription regulatory protein SNF2
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,56614
Polymers297,04911
Non-polymers5183
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 5 types, 9 molecules OAEBFCGDH

#1: 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Strain: ATCC 204508 / S288c / Gene: SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C / Production host: Escherichia coli (E. coli) / References: UniProt: P22082, EC: 3.6.4.-
#2: Protein/peptide Histone H3.2


Mass: 15303.930 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: P84233
#3: 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 (E. coli) / References: UniProt: P62799
#4: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#5: 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 (E. coli) / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (167-MER)


Mass: 51381.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (167-MER)


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

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Non-polymers , 3 types, 3 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium
#9: 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
#10: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

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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 / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: complex of snf2 and nucleosome in ADP BeFx state / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 2250 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1800 nm / Calibrated defocus min: 1800 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µns
Specimen holderCryogen: NITROGEN / 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) / Num. of grids imaged: 4 / Num. of real images: 4247
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 1-32

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82725 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.01117650
f_angle_d0.94925082
f_dihedral_angle_d19.08212286
f_chiral_restr0.0512856
f_plane_restr0.0062293

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