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- EMDB-3774: Cryo-EM structure of a human INO80 sub-complex (RuvBL1/2, Ino80) -

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Basic information

Entry
Database: EMDB / ID: EMD-3774
TitleCryo-EM structure of a human INO80 sub-complex (RuvBL1/2, Ino80)
Map dataSC2 INO80 subcomplex.
Sample
  • Complex: Human SC2 INO80 subcomplex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsAramayo RJ / Willhoft O / Ayala R / Bythell-Douglas R / Wigley D / Zhang X
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust098412/Z/12/Z United Kingdom
Wellcome Trust095519/Z/11/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Cryo-EM structures of the human INO80 chromatin-remodeling complex.
Authors: Ricardo J Aramayo / Oliver Willhoft / Rafael Ayala / Rohan Bythell-Douglas / Dale B Wigley / Xiaodong Zhang /
Abstract: Access to chromatin for processes such as transcription and DNA repair requires the sliding of nucleosomes along DNA. This process is aided by chromatin-remodeling complexes, such as the multisubunit ...Access to chromatin for processes such as transcription and DNA repair requires the sliding of nucleosomes along DNA. This process is aided by chromatin-remodeling complexes, such as the multisubunit INO80 chromatin-remodeling complex. Here we present cryo-EM structures of the active core complex of human INO80 at 9.6 Å, with portions at 4.1-Å resolution, and reconstructions of combinations of subunits. Together, these structures reveal the architecture of the INO80 complex, including Ino80 and actin-related proteins, which is assembled around a single RUVBL1 (Tip49a) and RUVBL2 (Tip49b) AAA+ heterohexamer. An unusual spoked-wheel structural domain of the Ino80 subunit is engulfed by this heterohexamer; both, in combination, form the core of the complex. We also identify a cleft in RUVBL1 and RUVBL2, which forms a major interaction site for partner proteins and probably communicates these interactions to its nucleotide-binding sites.
History
DepositionJun 21, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseDec 13, 2017-
UpdateApr 1, 2020-
Current statusApr 1, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3774.png

Downloads & links

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Map

FileDownload / File: emd_3774.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSC2 INO80 subcomplex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 70 pix.
= 231. Å		3.3 Å/pix.
x 70 pix.
= 231. Å		3.3 Å/pix.
x 70 pix.
= 231. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-0.816314 - 3.5456467
Average (Standard dev.)0.06357626 (±0.38393372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions707070
Spacing707070
CellA=B=C: 231.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.33.33.3
M x/y/z707070
origin x/y/z0.0000.0000.000
length x/y/z231.000231.000231.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707070
D min/max/mean-0.8163.5460.064

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Supplemental data

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Sample components

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Entire : Human SC2 INO80 subcomplex

EntireName: Human SC2 INO80 subcomplex
Components
  • Complex: Human SC2 INO80 subcomplex

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Supramolecule #1: Human SC2 INO80 subcomplex

SupramoleculeName: Human SC2 INO80 subcomplex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65705
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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