9S3R | pdb_00009s3r

Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB

• PDB DOI: https://doi.org/10.2210/pdb9S3R/pdb
• EM Map EMD-54549: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-25 Released: 2026-05-20 
• Deposition Author(s): Spiteri, V.A., Nakasone, M.A., Casement, R., Iso, K., Cowan, A.D., Ciulli, A.
• Funding Organization(s): Eisai, DSTT, H2020 Marie Curie Actions of the European Commission, European Research Council (ERC), Austrian Science Fund, Vienna Science and Technology Fund (WWTF), European Molecular Biology Organization (EMBO), Innovative Medicines Initiative, Fundacion Alfonso Martin Escudero, UK Research and Innovation (UKRI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dual E3 ligase recruitment by monovalent degraders enables redundant and tunable degradation of SMARCA2/4.

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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 178.24 kDa 
• Atom Count: 8,658 
• Modeled Residue Count: 1,084 
• Deposited Residue Count: 1,583 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	1,140	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
PHAROS:  Q16531 GTEx:  ENSG00000167986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 16	B	218	Homo sapiens	Mutation(s): 0  Gene Names: DCAF16, C4orf30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXF7 (Homo sapiens) Explore Q9NXF7  Go to UniProtKB:  Q9NXF7
PHAROS:  Q9NXF7 GTEx:  ENSG00000163257

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable global transcription activator SNF2L2	C	123	Homo sapiens	Mutation(s): 0  Gene Names: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens) Go to UniProtKB:  P51531
PHAROS:  P51531 GTEx:  ENSG00000080503

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DET1- and DDB1-associated protein 1	D	102	Homo sapiens	Mutation(s): 0  Gene Names: DDA1, C19orf58, PCIA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW61 (Homo sapiens) Explore Q9BW61  Go to UniProtKB:  Q9BW61
PHAROS:  Q9BW61 GTEx:  ENSG00000130311

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JLV( Subject of Investigation/LOI)	F [auth B]	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 C30 H37 N7 O SKFNVEPOSDRTJK-FDLQWACYSA-N
ZN	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC	v4.6.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-20 
Deposition Author(s): Spiteri, V.A., Nakasone, M.A., Casement, R., Iso, K., Cowan, A.D., Ciulli, A.

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Funding Organization	Location	Grant Number
Eisai	Japan	--
DSTT	United Kingdom	--
H2020 Marie Curie Actions of the European Commission	European Union	101024945
European Research Council (ERC)	European Union	851478
Austrian Science Fund	Austria	P7909
Austrian Science Fund	Austria	P36746
Austrian Science Fund	Austria	P5918723
Vienna Science and Technology Fund (WWTF)	Austria	LS21-015
European Molecular Biology Organization (EMBO)	European Union	283-2023
Innovative Medicines Initiative	Switzerland	875510
Fundacion Alfonso Martin Escudero	Spain	--
UK Research and Innovation (UKRI)	United Kingdom	EP/Z002176/1

Revision History  

• Version 1.0: 2026-05-20
  Type: Initial release