+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22265 | |||||||||||||||
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Title | Cryo-EM structure of BCL6 bound to BI-3802 | |||||||||||||||
Map data | Main map | |||||||||||||||
Sample |
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Keywords | transcription factor / degrader / TRANSCRIPTION | |||||||||||||||
Function / homology | Function and homology information 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 ...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 / negative regulation of B cell apoptotic process / positive regulation of cell motility / FOXO-mediated transcription of cell death genes / negative regulation of Rho protein signal transduction / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / cell morphogenesis / heterochromatin formation / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / protein localization / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / inflammatory response / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Yoon H / Burman SSR | |||||||||||||||
Funding support | United States, Switzerland, 4 items
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Citation | Journal: Nature / Year: 2020 Title: Small-molecule-induced polymerization triggers degradation of BCL6. Authors: Mikołaj Słabicki / Hojong Yoon / Jonas Koeppel / Lena Nitsch / Shourya S Roy Burman / Cristina Di Genua / Katherine A Donovan / Adam S Sperling / Moritz Hunkeler / Jonathan M Tsai / Rohan ...Authors: Mikołaj Słabicki / Hojong Yoon / Jonas Koeppel / Lena Nitsch / Shourya S Roy Burman / Cristina Di Genua / Katherine A Donovan / Adam S Sperling / Moritz Hunkeler / Jonathan M Tsai / Rohan Sharma / Andrew Guirguis / Charles Zou / Priya Chudasama / Jessica A Gasser / Peter G Miller / Claudia Scholl / Stefan Fröhling / Radosław P Nowak / Eric S Fischer / Benjamin L Ebert / Abstract: Effective and sustained inhibition of non-enzymatic oncogenic driver proteins is a major pharmacological challenge. The clinical success of thalidomide analogues demonstrates the therapeutic efficacy ...Effective and sustained inhibition of non-enzymatic oncogenic driver proteins is a major pharmacological challenge. The clinical success of thalidomide analogues demonstrates the therapeutic efficacy of drug-induced degradation of transcription factors and other cancer targets, but a substantial subset of proteins are resistant to targeted degradation using existing approaches. Here we report an alternative mechanism of targeted protein degradation, in which a small molecule induces the highly specific, reversible polymerization of a target protein, followed by its sequestration into cellular foci and subsequent degradation. BI-3802 is a small molecule that binds to the Broad-complex, Tramtrack and Bric-à-brac (BTB) domain of the oncogenic transcription factor B cell lymphoma 6 (BCL6) and leads to the proteasomal degradation of BCL6. We use cryo-electron microscopy to reveal how the solvent-exposed moiety of a BCL6-binding molecule contributes to a composite ligand-protein surface that engages BCL6 homodimers to form a supramolecular structure. Drug-induced formation of BCL6 filaments facilitates ubiquitination by the SIAH1 E3 ubiquitin ligase. Our findings demonstrate that a small molecule such as BI-3802 can induce polymerization coupled to highly specific protein degradation, which in the case of BCL6 leads to increased pharmacological activity compared to the effects induced by other BCL6 inhibitors. These findings open new avenues for the development of therapeutic agents and synthetic biology. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22265.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-22265-v30.xml emd-22265.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22265_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_22265.png | 39 KB | ||
Masks | emd_22265_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-22265.cif.gz | 7 KB | ||
Others | emd_22265_half_map_1.map.gz emd_22265_half_map_2.map.gz | 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22265 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22265 | HTTPS FTP |
-Validation report
Summary document | emd_22265_validation.pdf.gz | 802.8 KB | Display | EMDB validaton report |
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Full document | emd_22265_full_validation.pdf.gz | 802.4 KB | Display | |
Data in XML | emd_22265_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_22265_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22265 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22265 | HTTPS FTP |
-Related structure data
Related structure data | 6xmxMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22265.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22265_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: unfiltered half map (1) from refinement
File | emd_22265_half_map_1.map | ||||||||||||
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Annotation | unfiltered half map (1) from refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered half map (2) from refinement
File | emd_22265_half_map_2.map | ||||||||||||
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Annotation | unfiltered half map (2) from refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : B-cell lymphoma 6 protein (BCL6) filament
Entire | Name: B-cell lymphoma 6 protein (BCL6) filament |
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Components |
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-Supramolecule #1: B-cell lymphoma 6 protein (BCL6) filament
Supramolecule | Name: B-cell lymphoma 6 protein (BCL6) filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: BCL6 polymerized upon addition of small molecule BI-3802. 4 dimers enclosed in map. |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 352 KDa |
-Macromolecule #1: B-cell lymphoma 6 protein
Macromolecule | Name: B-cell lymphoma 6 protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.505305 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDWSHPQFEK SAVGLNDIFE AQKIEWHEGG GGSGENLYFQ GGGRADSCIQ FTRHASDVLL NLNRLRSRDI LTDVVIVVSR EQFRAHKTV LMACSGLFYS IFTDQLKCNL SVINLDPEIN PEGFCILLDF MYTSRLNLRE GNIMAVMATA MYLQMEHVVD T CRKFIKAS ...String: MDWSHPQFEK SAVGLNDIFE AQKIEWHEGG GGSGENLYFQ GGGRADSCIQ FTRHASDVLL NLNRLRSRDI LTDVVIVVSR EQFRAHKTV LMACSGLFYS IFTDQLKCNL SVINLDPEIN PEGFCILLDF MYTSRLNLRE GNIMAVMATA MYLQMEHVVD T CRKFIKAS EAEMVSAIKP PREEFLNSRM LMPQDIMAYR GCEVVENNLP LRSAPGCESR AFAPSLYSGL STPPASYSMY SH LPVSSLL FSDEEFRDVR MPVANPFPKE RALPCDSARP VPGEYSRPTL EVSPNVCHSN IYSPKETIPE EARSDMHYSV AEG LKPAAP SARNAPYFPC DKASKEEERP SSEDEIALHF EPPNAPLNRK GLVSPQSPQK SDCQPNSPTE SCSSKNACIL QASG UniProtKB: B-cell lymphoma 6 protein |
-Macromolecule #2: 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]py...
Macromolecule | Name: 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide type: ligand / ID: 2 / Number of copies: 8 / Formula: U52 |
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Molecular weight | Theoretical: 484.978 Da |
Chemical component information | ChemComp-U52: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.48 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP Details: 4 ul sample applied twice, blotted 1.3s each time. | ||||||||||||
Details | Strep II-Avi BCL6 (aa5-360) polymerized by addition of 1.5 molar excess BI-3802. CHAPSO (0.8 mM final) added for grid preparation. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Details | Data collection in counting mode, using multi shot scheme (4 holes per stage position, 2 shots per hole) |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 7553 / Average exposure time: 3.0 sec. / Average electron dose: 63.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 7-128 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Real_space_refine: global minimization, rigid body and adp refinement with target restraints. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-6xmx: |