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- EMDB-68927: The consensus map for the complete Chaetomium thermophilum RSC-NC... -

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Basic information

Entry
Database: EMDB / ID: EMD-68927
TitleThe consensus map for the complete Chaetomium thermophilum RSC-NCP complex
Map dataThe consensus map used for generating the composite map of the complete RSC-NCP complex
Sample
  • Complex: RSC
KeywordsSWI/SNF-family chromatin remodeling / RSC / PBAF / DNA BINDING PROTEIN / nucleosome
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.45 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
DepositionFeb 5, 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_68927.png

Downloads & links

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Map

FileDownload / File: emd_68927.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe consensus map used for generating the composite map of the complete RSC-NCP complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.24753277 - 0.730303
Average (Standard dev.)-0.00012242066 (±0.028651584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 445.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The consensus map processed by DeepEMhancer to improve density

Fileemd_68927_additional_1.map
AnnotationThe consensus map 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_68927_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_68927_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 : RSC

EntireName: RSC
Components
  • Complex: RSC

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Supramolecule #1: RSC

SupramoleculeName: RSC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Details: The RSC complex is overexpressed in 293F cells and purified by affinity chromatography, anion exchange chromatography, Grafix, etc.
Source (natural)Organism: Thermochaetoides thermophila (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 chloride
20.0 mMC8H18N2O4SHEPEs
0.5 mMC10H15N5O10P2ADP
1.0 mMBeSO4Beryllium sulfate
8.0 mMNaFsodium fluoride
VitrificationCryogen name: ETHANE
DetailsThis sample was homogenous 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

Particle selectionNumber selected: 754609
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 117380
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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