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

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Database: PDB / ID: 5x0y
TitleComplex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome
  • (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
Specimen sourceXenopus laevis / amphibia / African clawed frog / African clawed frog (Wikipedia) /
Saccharomyces cerevisiae / yeast / Wikipedia /
Synthetic construct
MethodElectron microscopy (4.69 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 Yorodumi Papers
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
1.1Apr 26, 2017Structure modelRefinement description
1.2Jun 7, 2017Structure modelDatabase references

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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

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


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
#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.-

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


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

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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

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


SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
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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