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- PDB-9s3r: Ternary complex structure of compound 1 bound to SMARCA2 bromodom... -

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Basic information

Entry
Database: PDB / ID: 9s3r
TitleTernary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
Components
  • DDB1- and CUL4-associated factor 16
  • DET1- and DDB1-associated protein 1
  • DNA damage-binding protein 1
  • Probable global transcription activator SNF2L2
KeywordsTRANSCRIPTION / Protein complex / covalent degrader / targeted protein degradation / E3 ligase
Function / homology
Function and homology information


bBAF complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / regulation of G0 to G1 transition ...bBAF complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / regulation of G0 to G1 transition / nucleosome array spacer activity / intermediate filament cytoskeleton / positive regulation by virus of viral protein levels in host cell / regulation of nucleotide-excision repair / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / UV-damage excision repair / positive regulation of T cell differentiation / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / positive regulation of double-strand break repair / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of stem cell population maintenance / ubiquitin ligase complex scaffold activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of reproductive process / negative regulation of developmental process / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / viral release from host cell / spermatid development / negative regulation of cell differentiation / cullin family protein binding / positive regulation of myoblast differentiation / ectopic germ cell programmed cell death / ATP-dependent activity, acting on DNA / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / helicase activity / nucleotide-excision repair / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / sperm end piece / negative regulation of cell growth / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / 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 / Wnt signaling pathway / RMTs methylate histone arginines / Formation of Incision Complex in GG-NER / protein polyubiquitination / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / nervous system development / heterochromatin formation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / sperm principal piece / Neddylation / sperm midpiece / histone binding / ubiquitin-dependent protein catabolic process / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / transcription coactivator activity / chromosome, telomeric region / transcription cis-regulatory region binding / protein ubiquitination / chromatin remodeling / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / chromatin / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive 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 / Glutamine-Leucine-Glutamine, 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 / Glutamine-Leucine-Glutamine, QLQ / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSpiteri, V.A. / Nakasone, M.A. / Casement, R. / Iso, K. / Cowan, A.D. / Ciulli, A.
Funding support Japan, United Kingdom, European Union, Austria, Switzerland, Spain, 12items
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: To Be Published
Title: Dual E3 ligase recruitment by monovalent degraders enables redundant and tunable degradation of SMARCA2/4.
Authors: Spiteri, V.A. / Segal, D. / Correa-Saez, A. / Iso, K. / Casement, R. / Munoz i Ordono, M. / Nakasone, M.A. / Sathe, G. / Schatz, C. / Peters, H. / Doward, M. / Kainacher, L. / Cowan, A.D. / ...Authors: Spiteri, V.A. / Segal, D. / Correa-Saez, A. / Iso, K. / Casement, R. / Munoz i Ordono, M. / Nakasone, M.A. / Sathe, G. / Schatz, C. / Peters, H. / Doward, M. / Kainacher, L. / Cowan, A.D. / Ciulli, A. / Winter, G.E.
History
DepositionJul 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: DDB1- and CUL4-associated factor 16
C: Probable global transcription activator SNF2L2
D: DET1- and DDB1-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,2446
Polymers177,6674
Non-polymers5772
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
#2: Protein DDB1- and CUL4-associated factor 16


Mass: 24333.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF16, C4orf30 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NXF7
#3: Protein Probable global transcription activator SNF2L2 / ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / ...ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / hBRM / SNF2-alpha / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2


Mass: 14380.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#4: Protein DET1- and DDB1-associated protein 1 / Placenta cross-immune reaction antigen 1 / PCIA-1


Mass: 11855.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDA1, C19orf58, PCIA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BW61

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-A1JLV / 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


Mass: 511.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37N7O / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
Type: COMPLEX / Entity ID: #4, #3, #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium ChlorideNaCl1
31 mMTCEPC9H15O6P1
40.01 %Lauryl maltose neopentyl glycolC47H88O221
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Final complex component concentrations applied to the grid after incubation: 20 uM DCAF16:DDB1 (delta BPB): DDA1 50 uM SMARCA2 60 uM GNE58
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Applied 3.5 uL of sample to grid. wait = 10 sec, drain = 0 sec, blot = 4 sec, blotForce = 4

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.6.0particle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARCv4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40820 / Symmetry type: POINT

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