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- PDB-9q03: Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760... -

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Basic information

Entry
Database: PDB / ID: 9q03
TitleCryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined)
Components
  • B-cell lymphoma 6 protein
  • Protein cereblon
KeywordsLIGASE / Cereblon / BCL6 / LDD / degrader / E3
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation ...negative regulation of monoatomic ion transmembrane transport / regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / positive regulation of cell motility / negative regulation of B cell apoptotic process / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of Rho protein signal transduction / erythrocyte development / FOXO-mediated transcription of cell death genes / locomotory exploration behavior / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of T cell proliferation / B cell proliferation / negative regulation of cellular senescence / negative regulation of cell-matrix adhesion / negative regulation of Notch signaling pathway / positive regulation of Wnt signaling pathway / regulation of immune response / negative regulation of protein-containing complex assembly / Rho protein signal transduction / positive regulation of B cell proliferation / positive regulation of neuron differentiation / regulation of cytokine production / cell-matrix adhesion / transcription corepressor binding / positive regulation of protein-containing complex assembly / cell motility / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell morphogenesis / sequence-specific double-stranded DNA binding / intracellular protein localization / heterochromatin formation / regulation of cell population proliferation / actin cytoskeleton organization / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / DNA-binding transcription factor binding / sequence-specific DNA binding / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / transcription by RNA polymerase II / protein ubiquitination / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / Golgi apparatus / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type
Similarity search - Domain/homology
: / B-cell lymphoma 6 protein / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsZhu, J. / Fang, W. / Pagarigan, B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J Med Chem / Year: 2025
Title: Discovery of Potent and Selective BCL6 Ligand-Directed Degrader (LDD), BCL6-760.
Authors: Hunter P Shunatona / Natalie Holmberg Douglas / Jayce Rhodes / William Thomas / Diogo Da Silva / Jim Gamez / Matt Groza / Andy Christoforou / Jinyi Zhu / Scott Johnson / Dharmpal Dodd / ...Authors: Hunter P Shunatona / Natalie Holmberg Douglas / Jayce Rhodes / William Thomas / Diogo Da Silva / Jim Gamez / Matt Groza / Andy Christoforou / Jinyi Zhu / Scott Johnson / Dharmpal Dodd / Dehua Huang / Jennifer Griffin / Giulianna Miseo / Brandon Whitefield / Dahlia Weiss / James Rader / Elif Kuzu / Jim Leisten / Joselyn Del Rosario / Lihong Shi / Mary Matyskiela / Philip P Chamberlain / Peter Belmont / Matt Alexander / Christoph W Zapf / Lynda Groocock / Deborah S Mortensen /
Abstract: The discovery of a potent and selective BCL6 ligand-directed degrader (LDD), BCL6-760 () is described. Through structure-activity relationships, the most potent heterobifunctional degraders of BCL6 ...The discovery of a potent and selective BCL6 ligand-directed degrader (LDD), BCL6-760 () is described. Through structure-activity relationships, the most potent heterobifunctional degraders of BCL6 were found to be those containing short aminopiperidine linkers in combination with an indazole-based cereblon (CRBN)-binding moiety (CBM). In vitro ADME profiling of potent molecules identified BCL6-760 as an ideal molecule for use in in vivo experiments due to its good passive permeability, solubility, and microsomal stability. Mechanistic studies confirmed that BCL6 degradation is CRBN mediated, and proteomic assessment indicates a clean and selective degradation profile. BCL6-760 exhibited good oral mouse PK and was capable of penetrant and sustained PD effects. At 60 mg/kg BID dosing, BCL6-760 achieves >90% BCL6 reduction and leads to an overall 64% tumor volume reduction in an OCI-LY-1 mouse xenograft efficacy model.
History
DepositionAug 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Remark 650HELIX DETERMINATION METHOD: MOE
Remark 700SHEET DETERMINATION METHOD: MOE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell lymphoma 6 protein
B: B-cell lymphoma 6 protein
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2265
Polymers86,4463
Non-polymers7812
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein B-cell lymphoma 6 protein / BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing ...BCL-6 / B-cell lymphoma 5 protein / BCL-5 / Protein LAZ-3 / Zinc finger and BTB domain-containing protein 27 / Zinc finger protein 51


Mass: 16431.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Plasmid: pMAL-c5x / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41182
#2: Protein Protein cereblon


Mass: 53581.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Cell (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1CM7 / (3R)-3-(6-{4-[(5-chloro-4-{[3-(3-hydroxy-3-methylbutyl)-1-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-5-yl]amino}pyrimidin-2-yl)(methyl)amino]piperidin-1-yl}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione


Mass: 715.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H43ClN10O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN
Nonpolymer detailsLIG DICTIONARY 94 100 Other LIG C1 C1 C 0 YNN 1 LIG C10 C10 C 0 YNN 2 LIG C11 C11 C 0 YNN 3 LIG C12 ...LIG DICTIONARY 94 100 Other LIG C1 C1 C 0 YNN 1 LIG C10 C10 C 0 YNN 2 LIG C11 C11 C 0 YNN 3 LIG C12 C12 C 0 YNN 4 LIG C13 C13 C 0 YNN 5 LIG C14 C14 C 0 YNN 6 LIG C15 C15 C 0 YNN 7 LIG C16 C16 C 0 YNN 8 LIG C17 C17 C 0 YNN 9 LIG C18 C18 C 0 NNN 10 LIG C19 C19 C 0 NNN 11 LIG C2 C2 C 0 YNN 12 LIG C20 C20 C 0 NNN 13 LIG C21 C21 C 0 NNN 14 LIG C22 C22 C 0 NNN 15 LIG C23 C23 C 0 NNN 16 LIG C24 C24 C 0 NNN 17 LIG C25 C25 C 0 NNN 18 LIG C26 C26 C 0 NNN 19 LIG C27 C27 C 0 NNR 20 LIG C28 C28 C 0 NNN 21 LIG C29 C29 C 0 NNN 22 LIG C3 C3 C 0 YNN 23 LIG C30 C30 C 0 NNN 24 LIG C31 C31 C 0 NNN 25 LIG C32 C32 C 0 NNN 26 LIG C33 C33 C 0 NNN 27 LIG C34 C34 C 0 NNN 28 LIG C35 C35 C 0 NNN 29 LIG C36 C36 C 0 NNN 30 LIG C4 C4 C 0 YNN 31 LIG C5 C5 C 0 YNN 32 LIG C6 C6 C 0 YNN 33 LIG C7 C7 C 0 YNN 34 LIG C8 C8 C 0 YNN 35 LIG C9 C9 C 0 YNN 36 LIG N1 N1 N 0 YNN 37 LIG N10 N10 N 0 NNN 38 LIG N2 N2 N 0 YNN 39 LIG N3 N3 N 0 YNN 40 LIG N4 N4 N 0 YNN 41 LIG N5 N5 N 0 NNN 42 LIG N6 N6 N 0 NNN 43 LIG N7 N7 N 0 NNN 44 LIG N8 N8 N 0 NNN 45 LIG N9 N9 N 0 NNN 46 LIG O1 O1 O 0 NNN 47 LIG O2 O2 O 0 NNN 48 LIG O3 O3 O 0 NNN 49 LIG O4 O4 O 0 NNN 50 LIG CL1 CL1 Cl 0 NNN 51 LIG H1 H1 H 0 NNN 52 LIG H2 H2 H 0 NNN 53 LIG H3 H3 H 0 NNN 54 LIG H10 H10 H 0 NNN 55 LIG H11 H11 H 0 NNN 56 LIG H12 H12 H 0 NNN 57 LIG H13 H13 H 0 NNN 58 LIG H14 H14 H 0 NNN 59 LIG H15 H15 H 0 NNN 60 LIG H16 H16 H 0 NNN 61 LIG H17 H17 H 0 NNN 62 LIG H18 H18 H 0 NNN 63 LIG H19 H19 H 0 NNN 64 LIG H20 H20 H 0 NNN 65 LIG H21 H21 H 0 NNN 66 LIG H22 H22 H 0 NNN 67 LIG H23 H23 H 0 NNN 68 LIG H24 H24 H 0 NNN 69 LIG H25 H25 H 0 NNN 70 LIG H26 H26 H 0 NNN 71 LIG H27 H27 H 0 NNN 72 LIG H28 H28 H 0 NNN 73 LIG H29 H29 H 0 NNN 74 LIG H30 H30 H 0 NNN 75 LIG H31 H31 H 0 NNN 76 LIG H32 H32 H 0 NNN 77 LIG H33 H33 H 0 NNN 78 LIG H34 H34 H 0 NNN 79 LIG H35 H35 H 0 NNN 80 LIG H36 H36 H 0 NNN 81 LIG H37 H37 H 0 NNN 82 LIG H38 H38 H 0 NNN 83 LIG H39 H39 H 0 NNN 84 LIG H4 H4 H 0 NNN 85 LIG H40 H40 H 0 NNN 86 LIG H41 H41 H 0 NNN 87 LIG H42 H42 H 0 NNN 88 LIG H43 H43 H 0 NNN 89 LIG H5 H5 H 0 NNN 90 LIG H6 H6 H 0 NNN 91 LIG H7 H7 H 0 NNN 92 LIG H8 H8 H 0 NNN 93 LIG H9 H9 H 0 NNN 94 LIG C1 C2 DOUB YN 1 LIG C1 C8 SING YN 2 LIG C1 H1 SING NN 3 LIG C10 C2 SING YN 4 LIG C10 C5 DOUB YN 5 LIG C10 N8 SING NN 6 LIG C11 C12 SING YN 7 LIG C11 C3 DOUB YN 8 LIG C11 N6 SING NN 9 LIG C12 C6 DOUB YN 10 LIG C12 N7 SING NN 11 LIG C13 C4 DOUB YN 12 LIG C13 C6 SING YN 13 LIG C13 N9 SING NN 14 LIG C14 C16 SING YN 15 LIG C14 C7 DOUB YN 16 LIG C14 CL1 SING NN 17 LIG C15 C27 SING NN 18 LIG C15 C8 SING YN 19 LIG C15 N2 DOUB YN 20 LIG C16 N3 DOUB YN 21 LIG C16 N9 SING NN 22 LIG C17 N1 DOUB YN 23 LIG C17 N10 SING NN 24 LIG C17 N3 SING YN 25 LIG C18 C21 SING NN 26 LIG C18 N5 SING NN 27 LIG C18 O1 DOUB NN 28 LIG C19 C27 SING NN 29 LIG C19 N5 SING NN 30 LIG C19 O2 DOUB NN 31 LIG C2 H2 SING NN 32 LIG C20 N6 SING NN 33 LIG C20 N7 SING NN 34 LIG C20 O3 DOUB NN 35 LIG C21 C22 SING NN 36 LIG C21 H8 SING NN 37 LIG C21 H9 SING NN 38 LIG C22 C27 SING NN 39 LIG C22 H10 SING NN 40 LIG C22 H11 SING NN 41 LIG C23 C25 SING NN 42 LIG C23 C28 SING NN 43 LIG C23 H12 SING NN 44 LIG C23 H13 SING NN 45 LIG C24 C26 SING NN 46 LIG C24 C28 SING NN 47 LIG C24 H14 SING NN 48 LIG C24 H15 SING NN 49 LIG C25 N8 SING NN 50 LIG C25 H16 SING NN 51 LIG C25 H17 SING NN 52 LIG C26 N8 SING NN 53 LIG C26 H18 SING NN 54 LIG C26 H19 SING NN 55 LIG C27 H20 SING NN 56 LIG C28 N10 SING NN 57 LIG C28 H21 SING NN 58 LIG C29 C36 SING NN 59 LIG C29 H22 SING NN 60 LIG C29 H23 SING NN 61 LIG C29 H24 SING NN 62 LIG C3 C4 SING YN 63 LIG C3 H3 SING NN 64 LIG C30 C36 SING NN 65 LIG C30 H25 SING NN 66 LIG C30 H26 SING NN 67 LIG C30 H27 SING NN 68 LIG C31 N4 SING NN 69 LIG C31 H28 SING NN 70 LIG C31 H29 SING NN 71 LIG C31 H30 SING NN 72 LIG C32 N6 SING NN 73 LIG C32 H31 SING NN 74 LIG C32 H32 SING NN 75 LIG C32 H33 SING NN 76 LIG C33 N10 SING NN 77 LIG C33 H34 SING NN 78 LIG C33 H35 SING NN 79 LIG C33 H36 SING NN 80 LIG C34 C35 SING NN 81 LIG C34 C36 SING NN 82 LIG C34 H37 SING NN 83 LIG C34 H38 SING NN 84 LIG C35 N7 SING NN 85 LIG C35 H39 SING NN 86 LIG C35 H40 SING NN 87 LIG C36 O4 SING NN 88 LIG C4 H4 SING NN 89 LIG C5 C9 SING YN 90 LIG C5 H5 SING NN 91 LIG C6 H6 SING NN 92 LIG C7 N1 SING YN 93 LIG C7 H7 SING NN 94 LIG C8 C9 DOUB YN 95 LIG C9 N4 SING YN 96 LIG N2 N4 SING YN 97 LIG N5 H41 SING NN 98 LIG N9 H42 SING NN 99 LIG O4 H43 SING NN 100 ZN DICTIONARY 1 0 Other ZN ZN ZN Zn 2 NNN 1

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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 of BCL6-CRBN-DDB1 with an LDD BCL6-760
Type: COMPLEX
Details: BCL6 BTB domain and CRBN/DDB1 was mixed with BCL6-760 in 1:1:1 ratio
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.162 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM(2-(4-(2-hydroxyethyl)piperazin-1-yl)ethanesulfonic acid)1
2200 mMsodium chlorideNaCl1
31 mMtris(2-carboxyethyl)phosphine1
40.25 %Dimethyl sulfoxide1
50.001 %Lauryl Maltose Neopentyl Glycol1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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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 magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.16 sec. / Electron dose: 35.18 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10236

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Topazparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8Cootmodel fitting
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 15859703
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112568 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
1pdb_00009dqd
1pdb_00009dqd1PDBexperimental model
2pdb_00005x9o
1pdb_00005x9o2PDBexperimental model
RefinementHighest resolution: 3.15 Å

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