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- PDB-5x0x: Complex of Snf2-Nucleosome complex with Snf2 bound to position +6... -

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Basic information

Entry
Database: PDB / ID: 5x0x
TitleComplex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome
DescriptorHistone H3.2
Histone H4
Histone H2A
Histone H2B 1.1
Transcription regulatory protein SNF2/DNA Complex
KeywordsSTRUCTURAL PROTEIN/HYDROLASE/DNA / Snf2 / nucleosome / chromatin remodeling / STRUCTURAL PROTEIN-HYDROLASE-DNA complex
Specimen sourceXenopus laevis / amphibia / African clawed frog /
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Synthetic construct
MethodElectron microscopy (3.97 Å resolution / Particle / Single particle)
AuthorsLi, M. / Liu, X. / Xia, X. / Chen, Z. / Li, X.
CitationNature, 2017, 544, 440-445

Nature, 2017, 544, 440-445 StrPapers
Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure.
Xiaoyu Liu / Meijing Li / Xian Xia / Xueming Li / Zhucheng Chen

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 23, 2017 / Release: Apr 19, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 19, 2017Structure modelrepositoryInitial release
1.1Jun 7, 2017Structure modelDatabase references

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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)298,45511
Polyers298,45511
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Polypeptide(L) , 5 types, 9 molecules AEBFCGDHO

#1: Polypeptide(L)Histone H3.2


Mass: 15421.101 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / References: UniProt: P84233

Cellular component

Molecular function

#2: Polypeptide(L)Histone H4


Mass: 11394.426 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / References: UniProt: P62799

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / References: UniProt: Q6AZJ8
#4: Polypeptide(L)Histone H2B 1.1 / H2B1.1


Mass: 13848.097 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / References: UniProt: P02281

Cellular component

Molecular function

#7: Polypeptide(L)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)
References: UniProt: P22082, EC: 3.6.4.-

Cellular component

Molecular function

Biological process

  • ATP-dependent chromatin remodeling (GO: 0043044)
  • cellular alcohol catabolic process (GO: 0044109)
  • chromatin remodeling (GO: 0006338)
  • DNA-dependent DNA replication (GO: 0006261)
  • double-strand break repair (GO: 0006302)
  • nucleosome mobilization (GO: 0042766)
  • positive regulation of cell adhesion involved in single-species biofilm formation (GO: 1900189)
  • positive regulation of invasive growth in response to glucose limitation (GO: 2000219)
  • positive regulation of mating type switching (GO: 0031496)
  • positive regulation of transcription from RNA polymerase II promoter (GO: 0045944)
  • positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation (GO: 0061412)
  • strand invasion (GO: 0042148)
  • sucrose catabolic process (GO: 0005987)
  • transcription, DNA-templated (GO: 0006351)

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chainDNA (167-MER)


Mass: 51381.758 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#6: DNA chainDNA (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 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

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Sample preparation

ComponentName: SHL6 complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / 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 FIELD / 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
IDNameVersionCategoryImage processing IDImaging ID
1e2boxer.py2PARTICLE SELECTION1
2UCSFImage4IMAGE ACQUISITION1
4CTFFind3CTF CORRECTION1
13Relion1.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 90725 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01117632
ELECTRON MICROSCOPYf_angle_d0.92625051
ELECTRON MICROSCOPYf_dihedral_angle_d19.07812287
ELECTRON MICROSCOPYf_chiral_restr0.0492856
ELECTRON MICROSCOPYf_plane_restr0.0052163

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