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- EMDB-71617: Cryo-EM map of BRD9-ZZ7-DCAF16/DDB1/DDA1 ternary complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71617
TitleCryo-EM map of BRD9-ZZ7-DCAF16/DDB1/DDA1 ternary complex
Map dataMain map
Sample
  • Complex: Ternary complex of BRD9-ZZ7-DCAF16/DDB1/DDA1
Keywordstargeted protein degradation / bromodomain / inhibitor / molecular glue / covalent / DCAF / E3 ligase / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsJin C / Baek K / Fischer E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA214608-09 United States
CitationJournal: To Be Published
Title: Cryo-EM map of BRD9-ZZ7-DCAF16/DDB1/DDA1 at 3 Angstroms resolution
Authors: Jin C / Baek K / Fischer E
History
DepositionJul 7, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71617.png

Downloads & links

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Map

FileDownload / File: emd_71617.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 512 pix.
= 376.832 Å		0.74 Å/pix.
x 512 pix.
= 376.832 Å		0.74 Å/pix.
x 512 pix.
= 376.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.736 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.23502341 - 0.41911215
Average (Standard dev.)0.00024579605 (±0.006614814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 376.832 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71617_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_71617_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for the main map

Fileemd_71617_half_map_1.map
AnnotationHalf map 1 for the main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for the main map

Fileemd_71617_half_map_2.map
AnnotationHalf map 2 for the main 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 : Ternary complex of BRD9-ZZ7-DCAF16/DDB1/DDA1

EntireName: Ternary complex of BRD9-ZZ7-DCAF16/DDB1/DDA1
Components
  • Complex: Ternary complex of BRD9-ZZ7-DCAF16/DDB1/DDA1

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Supramolecule #1: Ternary complex of BRD9-ZZ7-DCAF16/DDB1/DDA1

SupramoleculeName: Ternary complex of BRD9-ZZ7-DCAF16/DDB1/DDA1 / type: complex / ID: 1 / Parent: 0
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: 7.4
Component:
ConcentrationFormulaName
30.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
2.0 mMC9H15O6PTCEP

Details: 30 mM HEPES pH 7.4, 200 mM NaCl, 2 mM TCEP
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 11967 / Average exposure time: 2.52 sec. / Average electron dose: 53.685 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
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

DetailsMotion corrected as implemented in cryosparc live
Particle selectionNumber selected: 5417264
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Details: performed as in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 66613
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

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