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- EMDB-75625: SNAIL-GB1-LHC-Nucleosome complex (E-box in entry site) -

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Basic information

Entry
Database: EMDB / ID: EMD-75625
TitleSNAIL-GB1-LHC-Nucleosome complex (E-box in entry site)
Map data
Sample
  • Complex: Nucleosome-SNAIL-GB1-LHC complex
    • Complex: SNAIL-GB1
    • Complex: Histone octamer
    • Complex: LHC complex
Keywordstranscription factor / chromatin / histone / deacetylase / post-translational modifications / cancer / GENE REGULATION
Biological speciesHomo sapiens environmental sample (environmental samples) / Xenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsOsorio Valeriano M / Farnung L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM149229 United States
American Heart Association826614 United States
CitationJournal: To Be Published
Title: Multivalent Interactions Mediate SNAIL Transcription Factor Stimulation of the Nucleosome Deacetylase Activity of the CoREST Complex
Authors: Nam E / Osorio Valeriano M / Wang ZA / Whedon SD / Jiang H / Xinran Zhang M / Dubois-Coyne S / Haque IA / Jiang J / Ferreira J / Farnung L / Lee K / Cole PA
History
DepositionFeb 17, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75625.png

Downloads & links

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Map

FileDownload / File: emd_75625.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 440 pix.
= 484. Å		1.1 Å/pix.
x 440 pix.
= 484. Å		1.1 Å/pix.
x 440 pix.
= 484. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0772
Minimum - Maximum-0.23553267 - 0.6479016
Average (Standard dev.)-0.00023577349 (±0.013454865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 484.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75625_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75625_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75625_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleosome-SNAIL-GB1-LHC complex

EntireName: Nucleosome-SNAIL-GB1-LHC complex
Components
  • Complex: Nucleosome-SNAIL-GB1-LHC complex
    • Complex: SNAIL-GB1
    • Complex: Histone octamer
    • Complex: LHC complex

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Supramolecule #1: Nucleosome-SNAIL-GB1-LHC complex

SupramoleculeName: Nucleosome-SNAIL-GB1-LHC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4

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Supramolecule #2: SNAIL-GB1

SupramoleculeName: SNAIL-GB1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens environmental sample (environmental samples)

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Supramolecule #3: Histone octamer

SupramoleculeName: Histone octamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 109 KDa

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Supramolecule #4: LHC complex

SupramoleculeName: LHC complex / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4 / Details: LSD1-HDAC1-CoREST
Source (natural)Organism: Homo sapiens (human)

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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 / Details: HEPES pH 7.5, 50 mM NaCl, and 1 mM TCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4.0 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Particle selectionNumber selected: 295894
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 11979
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Avg.num./class: 14190
FSC plot (resolution estimation)

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