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- PDB-9rsd: Ternary complex of a charged molecular glue degrader ZZ1-SO2H, BR... -

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Basic information

Entry
Database: PDB / ID: 9rsd
TitleTernary complex of a charged molecular glue degrader ZZ1-SO2H, BRD4(BD1) neosubstrate, and the CTLH E3 ligase receptor module YPEL5-WDR26
Components
  • Bromodomain-containing protein 4
  • Protein yippee-like 5
  • WD repeat-containing protein 26
KeywordsLIGASE / E3 ubiquitin ligase / CTLH / GID / YPEL5 / Molecular Glue Degrader / Targeted Protein Degradation
Function / homology
Function and homology information


GID complex / mitotic spindle pole / histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / histone H3K9ac reader activity / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity ...GID complex / mitotic spindle pole / histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / histone H3K9ac reader activity / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / ubiquitin ligase complex / RNA polymerase II CTD heptapeptide repeat kinase activity / Regulation of pyruvate metabolism / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / tertiary granule lumen / chromosome / regulation of inflammatory response / midbody / histone binding / Potential therapeutics for SARS / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / cell population proliferation / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / Neutrophil degranulation / chromatin binding / regulation of transcription by RNA polymerase II / centrosome / positive regulation of DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Yippee domain / Yippee family / Yippee domain profile. / : / : / LisH-like dimerisation domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Yippee/Mis18/Cereblon ...Yippee domain / Yippee family / Yippee domain profile. / : / : / LisH-like dimerisation domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Bromodomain-containing protein 4 / Protein yippee-like 5 / WD repeat-containing protein 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsChrustowicz, J. / Schulman, B.A.
Funding support Germany, European Union, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3196/1-1 Germany
European Research Council (ERC)UPSmeetMet, 101098161European Union
Max Planck Society Germany
CitationJournal: To Be Published
Title: Molecular Glue Prodrug Discovery Enabled by Targeted Degron Display
Authors: Zhuang, Z. / Woong Sub, B. / Chrustowicz, J. / Kozicka, Z. / Hinshaw, S.M. / Li, V.L. / Donovan, K.A. / Sepic, S. / You, I. / Slabicki, M. / Fischer, E.S. / Ebert, B.L. / Schulman, B.A. / Gray, N.S.
History
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 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

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Assembly

Deposited unit
7: WD repeat-containing protein 26
W: WD repeat-containing protein 26
Y: Protein yippee-like 5
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,0038
Polymers170,1674
Non-polymers8364
Water362
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 , 3 types, 4 molecules 7WYB

#1: Protein WD repeat-containing protein 26 / CUL4- and DDB1-associated WDR protein 2 / Myocardial ischemic preconditioning up-regulated protein 2


Mass: 70539.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR26, CDW2, MIP2, PRO0852 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H7D7
#2: Protein Protein yippee-like 5


Mass: 13860.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YPEL5, CGI-127 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P62699
#3: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15226.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first bromodomain (BD1) of BRD4. The GGSGS sequence is a linker between BD1 and the upstream TEV cleavage site.
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1IL9 / 2-chloranyl-4-[[4-[(9S)-4,5,13-trimethyl-9-[2-[(2-methylpropan-2-yl)oxy]-2-oxidanylidene-ethyl]-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-7-yl]phenyl]carbamoyl]benzenesulfinic acid


Mass: 640.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30ClN5O5S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: ZZ1-SO2H-induced complex between YPEL5-CTLH E3 ligase and the first bromodomain (BD1) of BRD4
Type: COMPLEX
Details: The YPEL5-CTLH complex consists of TWA1, RANBP9, RMND5A, MAEA, WDR26, and YPEL5.
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample mixed with 0.1% beta-OG right before plunging
VitrificationCryogen name: NITROGEN

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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: 2300 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 65.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
9PHENIX1.21.1_5286model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 893388
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20764 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18QBN

8qbn

18QBN1PDBexperimental model
23MXF

3mxf

13MXF2PDBexperimental model
RefinementHighest resolution: 3.38 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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