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- EMDB-53544: Drosophila MSL HAT nucleosome complex H4K16ac postcatalytic H3K36... -

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Basic information

Entry
Database: EMDB / ID: EMD-53544
TitleDrosophila MSL HAT nucleosome complex H4K16ac postcatalytic H3K36me3 reader state focused refinement
Map dataFocused refinement map
Sample
  • Complex: MSL HAT nucleosome complex H4K16Ac postcatalytic H3K36me3 reader state
KeywordsHistone Acetyltransferase Complex / NUCLEAR PROTEIN
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMueller M / Kolesnikova O / Doudin M / Hoffmann T / Becker P / Eustermann S
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Be1140/9-1 Germany
German Research Foundation (DFG)Be1140/11-1 Germany
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: To Be Published
Title: To Be Published
Authors: Mueller M / Kolesnikova O / Doudin M / Thomae AW / Campos-Sparr A / Kraus S / Hoffmann T / Becker P / Eustermann S
History
DepositionMay 1, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53544.png

Downloads & links

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Map

FileDownload / File: emd_53544.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0045
Minimum - Maximum-0.012904236 - 0.029013753
Average (Standard dev.)0.000115549614 (±0.0010146025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53544_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_53544_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53544_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_53544_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 : MSL HAT nucleosome complex H4K16Ac postcatalytic H3K36me3 reader state

EntireName: MSL HAT nucleosome complex H4K16Ac postcatalytic H3K36me3 reader state
Components
  • Complex: MSL HAT nucleosome complex H4K16Ac postcatalytic H3K36me3 reader state

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Supramolecule #1: MSL HAT nucleosome complex H4K16Ac postcatalytic H3K36me3 reader state

SupramoleculeName: MSL HAT nucleosome complex H4K16Ac postcatalytic H3K36me3 reader state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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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

Concentration0.41 mg/mL
BufferpH: 7.5
Details: 0.5 mM Acetyl CoA, 0.05% beta octyl glucoside, 2 mM Hepes pH7.5, 5 mM KCl, 1 uM ZnCl2, 0.05 mM DTT, 17.5 mM TrisHCl, pH 7.5 35 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
DetailsFor CryoEM vitrication, the MSL-HAT core complex and H3K36me3 modified mononucleosomes were incubated in a 1:1.1 ratio with 0.5 mM Acetyl-CoA for 5-10 min on ice

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 54.97 e/Å2
Electron beamAcceleration voltage: 300 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 / Nominal magnification: 130000
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: 2012780
Details: WARP pretrained BoxNet2Mask_20180918 model, TOPAZ trained model, RELION 3D reference based picking
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 50532
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.4.1) / Details: cryoSPARC ab initio model generation
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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