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- EMDB-53934: Focus refined map of Human SAGA SF3B module -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-53934
TitleFocus refined map of Human SAGA SF3B module
Map data
Sample
  • Complex: SAGA
KeywordsTranscription co-activator / Lysine acetyltransferase / complex / TRANSCRIPTION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsDamilot M / Ben-Shem A / Papai G
Funding support France, 2 items
OrganizationGrant numberCountry
La ligue contre le cancer France
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0013 France
CitationJournal: Sci Adv / Year: 2026
Title: Insights into the structure and evolution of the human SAGA complex by affinity-ligand purification.
Authors: Mylène Damilot / Thomas Schoeps / Laszlo Tora / Patrick Schultz / Luc Lebeau / Gabor Papai / Adam Ben-Shem /
Abstract: Human SAGA is a 20-subunit transcriptional coactivator. Compared with yeast, metazoan SAGA uniquely incorporates a 150-kDa splicing-factor module (SPL), also present in U2 small nuclear ...Human SAGA is a 20-subunit transcriptional coactivator. Compared with yeast, metazoan SAGA uniquely incorporates a 150-kDa splicing-factor module (SPL), also present in U2 small nuclear ribonucleoprotein (U2snRNP). Metazoan gene duplication further specialized shared TFIID/SAGA subunits into SAGA-specific paralogs (TAF5L and TAF6L), but the functional consequences of this divergence are unknown. We report the structure of endogenous human SAGA purified via an affinity ligand from cells that were not disturbed by any genomic engineering tools. Our work reveals the high-resolution structure of SPL and the TAF6L HEAT repeat domain that provides the SPL with a docking surface. We elucidate how SPL and the HEAT repeats are incorporated into SAGA. We identify major structural differences between TAF6L/TAF5L and their canonical paralogs that enable SPL accommodation. SPL engages SAGA through a substantially smaller interface than in U2snRNP, despite sharing a deeply inserted helical motif. The seemingly weaker interaction of SPL with SAGA raises the possibility that SAGA relays this module to the splicing machinery.
History
DepositionJun 2, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53934.png

Downloads & links

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Map

FileDownload / File: emd_53934.map.gz / Format: CCP4 / Size: 259.1 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 Å/pix.
x 408 pix.
= 408. Å		1 Å/pix.
x 408 pix.
= 408. Å		1 Å/pix.
x 408 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.22054537 - 19.574427
Average (Standard dev.)-0.0072393217 (±0.2838981)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53934_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53934_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53934_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 : SAGA

EntireName: SAGA
Components
  • Complex: SAGA

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Supramolecule #1: SAGA

SupramoleculeName: SAGA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Homo sapiens (human) / Strain: K562
Molecular weightTheoretical: 1.6 MDa

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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

Concentration0.15 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1027610
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 59421
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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