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- EMDB-69475: The focused refined map for RSC-specific lobe of the Chaetomium t... -

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Basic information

Entry
Database: EMDB / ID: EMD-69475
TitleThe focused refined map for RSC-specific lobe of the Chaetomium thermophilum RSC complex
Map dataFocused refined map for RSC-specific lobe
Sample
  • Complex: The Chaetomium thermophilum RSC complex
KeywordsSWI/SNF-family chromatin remodeling / RSC / PBAF / DNA BINDING PROTEIN / nucleosome / NUCLEAR PROTEIN
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.72 Å
AuthorsMa SS / Liu MD / Shen QT / Chen Y
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2023YFA1800403 China
CitationJournal: Sci Adv / Year: 2026
Title: Structural principles underlying the evolution of SWI/SNF chromatin remodelers
Authors: Ma SS / Liu MD / Xu WC / Wang QM / Wang XM / Huang YG / Li MC / Li CH / Shen QT / Chen Y
History
DepositionMar 2, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69475.png

Downloads & links

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Map

FileDownload / File: emd_69475.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refined map for RSC-specific lobe
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.276
Minimum - Maximum-0.8827092 - 1.0327593
Average (Standard dev.)-0.0034766581 (±0.024835838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Focused refined map for RSC-specific lobe processed by...

Fileemd_69475_additional_1.map
AnnotationFocused refined map for RSC-specific lobe processed by DeepEMhancer to improve density
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_69475_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_69475_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The Chaetomium thermophilum RSC complex

EntireName: The Chaetomium thermophilum RSC complex
Components
  • Complex: The Chaetomium thermophilum RSC complex

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Supramolecule #1: The Chaetomium thermophilum RSC complex

SupramoleculeName: The Chaetomium thermophilum RSC complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
30.0 mMKClPotassium chloride
2.0 mMMgCl2Magnesium choloride
20.0 mMC8H18N2O4SHEPES
0.5 mMC10H15N5O10P2ADP
1.0 mMBeSO4Beryllium sulfate
8.0 mMNaFSodium Fluoride
VitrificationCryogen name: ETHANE
DetailsThe sample was homogeneous and monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 30165
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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