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- EMDB-54549: Ternary complex structure of compound 1 bound to SMARCA2 bromodom... -

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Entry
Database: EMDB / ID: EMD-54549
TitleTernary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
Map data
Sample
  • Complex: Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
    • Protein or peptide: DET1- and DDB1-associated protein 1
    • Protein or peptide: Probable global transcription activator SNF2L2
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 16
  • Ligand: ZINC ION
  • Ligand: 2-[6-azanyl-5-[(1~{S},5~{R})-8-[2-[(~{E})-3-(azepan-1-yl)prop-1-enyl]pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol
KeywordsProtein complex / covalent degrader / targeted protein degradation / TRANSCRIPTION / E3 ligase
Function / homology
Function and homology information


nBAF complex / npBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / nucleosome array spacer activity / regulation of G0 to G1 transition / positive regulation by virus of viral protein levels in host cell / SWI/SNF complex ...nBAF complex / npBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / nucleosome array spacer activity / regulation of G0 to G1 transition / positive regulation by virus of viral protein levels in host cell / SWI/SNF complex / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / biological process involved in interaction with symbiont / regulation of nucleotide-excision repair / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding / positive regulation of stem cell population maintenance / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of cellular response to stress / viral release from host cell / cullin family protein binding / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / positive regulation of gluconeogenesis / regulation of G1/S transition of mitotic cell cycle / regulation of embryonic development / replication fork processing / helicase activity / positive regulation of cell differentiation / proteasomal protein catabolic process / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / epigenetic regulation of gene expression / negative regulation of cell growth / nucleotide-excision repair / regulation of autophagy / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / cell population proliferation / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / protein polyubiquitination / Formation of Incision Complex in GG-NER / RMTs methylate histone arginines / positive regulation of protein catabolic process / cellular response to UV / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / rhythmic process / regulation of cell population proliferation / site of double-strand break / nervous system development / Neddylation / heterochromatin formation / spermatogenesis / ubiquitin-dependent protein catabolic process / histone binding / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein-macromolecule adaptor activity / chromosome, telomeric region / transcription coactivator activity / transcription cis-regulatory region binding / protein ubiquitination / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA repair / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / DNA damage response / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex binding / chromatin / negative regulation of transcription by RNA polymerase II
Similarity search - Function
DDB1- and CUL4-associated factor 16 / DDB1- and CUL4-associated factor 16 / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ ...DDB1- and CUL4-associated factor 16 / DDB1- and CUL4-associated factor 16 / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / Det1 complexing ubiquitin ligase / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 / DNA damage-binding protein 1 / DET1- and DDB1-associated protein 1 / DDB1- and CUL4-associated factor 16
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSpiteri VA / Nakasone MA / Casement R / Iso K / Cowan AD / Ciulli A
Funding support Japan, United Kingdom, European Union, Austria, Switzerland, Spain, 12 items
OrganizationGrant numberCountry
Eisai Japan
DSTT United Kingdom
H2020 Marie Curie Actions of the European Commission101024945European Union
European Research Council (ERC)851478European Union
Austrian Science FundP7909 Austria
Austrian Science FundP36746 Austria
Austrian Science FundP5918723 Austria
Vienna Science and Technology Fund (WWTF)LS21-015 Austria
European Molecular Biology Organization (EMBO)283-2023European Union
Innovative Medicines Initiative875510 Switzerland
Fundacion Alfonso Martin Escudero Spain
UK Research and Innovation (UKRI)EP/Z002176/1 United Kingdom
CitationJournal: Nat Chem Biol / Year: 2026
Title: Dual E3 ligase recruitment by monovalent degraders for tunable SMARCA 2/4 degradation.
Authors: Valentina A Spiteri / Dmitri Segal / Alejandro Correa-Sáez / Kentaro Iso / Ryan Casement / Miquel Muñoz I Ordoño / Mark A Nakasone / Gajanan Sathe / Caroline Schätz / Hannah E Peters / ...Authors: Valentina A Spiteri / Dmitri Segal / Alejandro Correa-Sáez / Kentaro Iso / Ryan Casement / Miquel Muñoz I Ordoño / Mark A Nakasone / Gajanan Sathe / Caroline Schätz / Hannah E Peters / Mark Doward / Lisa Kainacher / Angus D Cowan / Alessio Ciulli / Georg E Winter /
Abstract: Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) target proteins for degradation by co-opting an E3 ligase. While heterotrivalent PROTACs that can recruit multiple E3 ...Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) target proteins for degradation by co-opting an E3 ligase. While heterotrivalent PROTACs that can recruit multiple E3 ligases have been described, all MGDs reported to date depend on a single E3. Using orthogonal genetic screening, biophysical and structural analyses, we show that a monovalent MGD can recruit CUL4 and CRL1 in parallel to degrade SMARCA2/4. Deep mutational scanning identifies C173 in DCAF16 as essential for degrader activity and intact protein mass spectrometry confirms covalent modification at this site. Elucidating the ternary complex structure reveals a unique binding mode and a distinct interface of neointeractions that underlie degrader specificity. We demonstrate that ligase dependency is chemically and genetically tunable. Minimal compound modifications shift preference from DCAF16 to FBXO22, while a single substitution boosts degrader dependency on DCAF16. These results establish a framework for designing tunable dual E3 ligase degraders to mitigate potential resistance mechanisms.
History
DepositionJul 25, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54549.png

Downloads & links

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Map

FileDownload / File: emd_54549.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 400 pix.
= 412. Å		1.03 Å/pix.
x 400 pix.
= 412. Å		1.03 Å/pix.
x 400 pix.
= 412. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0633
Minimum - Maximum-0.276643 - 0.50294936
Average (Standard dev.)-0.0003939873 (±0.009033351)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 412.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54549_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_54549_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ternary complex structure of compound 1 bound to SMARCA2 bromodom...

EntireName: Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
Components
  • Complex: Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
    • Protein or peptide: DET1- and DDB1-associated protein 1
    • Protein or peptide: Probable global transcription activator SNF2L2
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 16
  • Ligand: ZINC ION
  • Ligand: 2-[6-azanyl-5-[(1~{S},5~{R})-8-[2-[(~{E})-3-(azepan-1-yl)prop-1-enyl]pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol

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Supramolecule #1: Ternary complex structure of compound 1 bound to SMARCA2 bromodom...

SupramoleculeName: Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4, #3, #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.097469 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...String:
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGI HEHA SIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFCGNVAH QQLIQITSAS VRLVS QEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVACLDIT PLGDSNGLSP LCAIGL WTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIETGLL SDRKKVTLGT QPTVLRT FR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLTIG TIDEIQKLHI RTVPLYES P RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME GNFEEIARDF NPNWMSAVEI L DDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LV TSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGM KREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #2: DDB1- and CUL4-associated factor 16

MacromoleculeName: DDB1- and CUL4-associated factor 16 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.333449 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGMGPRNPSP DHLSESESEE EENISYLNES SGEEWDSSEE EDSMVPNLSP LESLAWQVKC LLKYSTTWKP LNPNSWLYHA KLLDPSTPV HILREIGLRL SHCSHCVPKL EPIPEWPPLA SCGVPPFQKP LTSPSRLSRD HATLNGALQF ATKQLSRTLS R ATPIPEYL ...String:
GGMGPRNPSP DHLSESESEE EENISYLNES SGEEWDSSEE EDSMVPNLSP LESLAWQVKC LLKYSTTWKP LNPNSWLYHA KLLDPSTPV HILREIGLRL SHCSHCVPKL EPIPEWPPLA SCGVPPFQKP LTSPSRLSRD HATLNGALQF ATKQLSRTLS R ATPIPEYL KQIPNSCVSG CCCGWLTKTV KETTRTEPIN TTYSYTDFQK AVNKLLTASL

UniProtKB: DDB1- and CUL4-associated factor 16

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Macromolecule #3: Probable global transcription activator SNF2L2

MacromoleculeName: Probable global transcription activator SNF2L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.380542 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SMAEKLSPNP PKLTKQMNAI IDTVINYKDS SGRQLSEVFI QLPSRKELPE YYELIRKPVD FKKIKERIRN HKYRSLGDLE KDVMLLCHN AQTFNLEGSQ IYEDSIVLQS VFKSARQKIA KEEE

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2

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Macromolecule #4: DET1- and DDB1-associated protein 1

MacromoleculeName: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.855297 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRK VARTDSPDMH EDT

UniProtKB: DET1- and DDB1-associated protein 1

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: 2-[6-azanyl-5-[(1~{S},5~{R})-8-[2-[(~{E})-3-(azepan-1-yl)prop-1-e...

MacromoleculeName: 2-[6-azanyl-5-[(1~{S},5~{R})-8-[2-[(~{E})-3-(azepan-1-yl)prop-1-enyl]pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1JLV
Molecular weightTheoretical: 511.661 Da

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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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium Chloride
1.0 mMC9H15O6PTCEP
0.01 %C47H88O22Lauryl maltose neopentyl glycol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Applied 3.5 uL of sample to grid. wait = 10 sec, drain = 0 sec, blot = 4 sec, blotForce = 4.
DetailsFinal complex component concentrations applied to the grid after incubation: 20 uM DCAF16:DDB1 (delta BPB): DDA1 50 uM SMARCA2 60 uM GNE58

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8g46

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.0) / Number images used: 40820
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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