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- EMDB-38864: RSF-38N38NCP complex Class0 -

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Basic information

Entry
Database: EMDB / ID: EMD-38864
TitleRSF-38N38NCP complex Class0
Map data
Sample
  • Complex: structure of RSF-38N38 NCP complex Class 0
KeywordsISWI chromatin remodeling complex / DNA BINDING PROTEIN
Biological speciesHeardaxius (crustacean)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.91 Å
AuthorsZhang JL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U20A2013, 32241021 and 32170189 China
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2024
Title: Cryo-EM structure and functional analysis of the chromatin remodeler RSF.
Authors: Jiale Zhang / Heyu Zhao / Binqian Zou / Huadong Li / Shuqi Dong / Jiali Guan / Chi Wang / Weijie Li / Yutong Liu / Yingying Chen / Nadia Rasheed / Jun He /
Abstract: The RSF complex belongs to the ISWI chromatin-remodeling family and is composed of two subunits: RSF1 (remodeling and spacing factor 1) and SNF2h (sucrose nonfermenting protein 2 homolog). The RSF ...The RSF complex belongs to the ISWI chromatin-remodeling family and is composed of two subunits: RSF1 (remodeling and spacing factor 1) and SNF2h (sucrose nonfermenting protein 2 homolog). The RSF complex participates in nucleosome spacing and assembly, and subsequently promotes nucleosome maturation. Although SNF2h has been extensively studied in the last few years, the structural and functional properties of the remodeler RSF1 still remain vague. Here, a cryo-EM structure of the RSF-nucleosome complex is reported. The 3D model shows a two-lobe architecture of RSF, and the structure of the RSF-nucleosome (flanked with linker DNA) complex shows that the RSF complex moves the DNA away from the histone octamer surface at the DNA-entry point. Additionally, a nucleosome-sliding assay and a restriction-enzyme accessibility assay show that the RSF1 subunit may cause changes in the chromatin-remodeling properties of SNF2h. As a `nucleosome ruler', the results of an RSF-dinucleosome binding affinity test led to the proposal that the critical distance that RSF `measures' between two nucleosomes is about 24 base pairs.
History
DepositionJan 27, 2024-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38864.png

Downloads & links

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Map

FileDownload / File: emd_38864.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 512 pix.
= 450.56 Å		0.88 Å/pix.
x 512 pix.
= 450.56 Å		0.88 Å/pix.
x 512 pix.
= 450.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.052
Minimum - Maximum-0.04019216 - 0.3299133
Average (Standard dev.)-0.00020148784 (±0.008100997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38864_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38864_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : structure of RSF-38N38 NCP complex Class 0

EntireName: structure of RSF-38N38 NCP complex Class 0
Components
  • Complex: structure of RSF-38N38 NCP complex Class 0

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Supramolecule #1: structure of RSF-38N38 NCP complex Class 0

SupramoleculeName: structure of RSF-38N38 NCP complex Class 0 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Heardaxius (crustacean)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18952
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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