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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: Nucleic Acids Res / Year: 2026
Title: Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.
Authors: Eunju Nam / Manuel Osorio Valeriano / Zhipeng A Wang / Samuel D Whedon / Hanjie Jiang / Maggie Xinran Zhang / Sarah DuBois-Coyne / Ishraq A Haque / Jennifer Jiang / Jennifer Ferreira / Lucas ...Authors: Eunju Nam / Manuel Osorio Valeriano / Zhipeng A Wang / Samuel D Whedon / Hanjie Jiang / Maggie Xinran Zhang / Sarah DuBois-Coyne / Ishraq A Haque / Jennifer Jiang / Jennifer Ferreira / Lucas Farnung / Kwangwoon Lee / Philip A Cole /
Abstract: SNAIL is a transcription factor that plays a role in development and cancer. SNAIL contains an N-terminal SNAG domain that is a high-affinity ligand for the histone substrate binding lysine-specific ...SNAIL is a transcription factor that plays a role in development and cancer. SNAIL contains an N-terminal SNAG domain that is a high-affinity ligand for the histone substrate binding lysine-specific demethylase 1 (LSD1). SNAIL also contains a C-terminal zinc finger domain that binds to DNA E-box sequences. SNAIL and related transcription factor family members are known to recruit LSD1-containing protein complexes to specific sites in chromatin to regulate gene expression. LSD1 can form a multiprotein complex with histone deacetylase 1 (HDAC1) and CoREST scaffolding protein (LHC). In this study, we use a purified system to analyze the role of SNAIL in modulating nucleosome deacetylation by the LHC complex. We find that SNAIL enhances nucleosome deacetylase activity of the LHC complex at multiple histone H3 sites through multivalent interactions. Enhanced nucleosome deacetylation is dependent on SNAIL's SNAG and zinc finger domains. Unexpectedly, we find that SNAIL-stimulated nucleosome deacetylation by LHC also involves interactions of the nucleosome histone acidic patch, including histone H2A acidic residues. Modeling and mutagenesis experiments suggest that this acidic patch could engage a basic patch in the disordered segment of LSD1. Together, these findings reveal how a transcription factor can influence a cascade of molecular recognition events to regulate chromatin structure.
History
DepositionFeb 17, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 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

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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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
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Half map: #2

Fileemd_75625_half_map_1.map
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Half map: #1

Fileemd_75625_half_map_2.map
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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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