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- EMDB-41424: Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-41424
TitleCryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1
Map datamain map
Sample
  • Complex: Ternary Complex of DDB1dB:CRBN:PT-179 with SD40
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,SD40
  • Ligand: ZINC ION
  • Ligand: 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione
Keywordsubiquitin / CRBN / directed evolution / Zinc finger / IMiD / Molecular glue / TRANSFERASE
Function / homology
Function and homology information


lymphocyte differentiation / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / NOTCH3 Intracellular Domain Regulates Transcription / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding ...lymphocyte differentiation / negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / NOTCH3 Intracellular Domain Regulates Transcription / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / detection of maltose stimulus / maltose transport complex / negative regulation of reproductive process / mesoderm development / negative regulation of developmental process / carbohydrate transport / locomotory exploration behavior / cullin family protein binding / viral release from host cell / carbohydrate transmembrane transporter activity / maltose binding / positive regulation of Wnt signaling pathway / maltose transport / maltodextrin transmembrane transport / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / pericentric heterochromatin / proteasomal protein catabolic process / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of gluconeogenesis / ATP-binding cassette (ABC) transporter complex / erythrocyte differentiation / cell chemotaxis / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Wnt signaling pathway / 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 / site of double-strand break / Neddylation / outer membrane-bounded periplasmic space / chromatin organization / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transmembrane transporter binding / periplasmic space / chromosome, telomeric region / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / extracellular space / DNA binding / extracellular exosome / 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) ...: / 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) / 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 / PUA-like superfamily / Zinc finger, C2H2 type / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / zinc finger / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / DNA-binding protein Ikaros / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsRoy Burman SS / Hunkeler M / Fischer ES
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA214608 United States
Cancer Research Institute United States
CitationJournal: Science / Year: 2024
Title: Continuous evolution of compact protein degradation tags regulated by selective molecular glues.
Authors: Jaron A M Mercer / Stephan J DeCarlo / Shourya S Roy Burman / Vedagopuram Sreekanth / Andrew T Nelson / Moritz Hunkeler / Peter J Chen / Katherine A Donovan / Praveen Kokkonda / Praveen K ...Authors: Jaron A M Mercer / Stephan J DeCarlo / Shourya S Roy Burman / Vedagopuram Sreekanth / Andrew T Nelson / Moritz Hunkeler / Peter J Chen / Katherine A Donovan / Praveen Kokkonda / Praveen K Tiwari / Veronika M Shoba / Arghya Deb / Amit Choudhary / Eric S Fischer / David R Liu /
Abstract: Conditional protein degradation tags (degrons) are usually >100 amino acids long or are triggered by small molecules with substantial off-target effects, thwarting their use as specific modulators of ...Conditional protein degradation tags (degrons) are usually >100 amino acids long or are triggered by small molecules with substantial off-target effects, thwarting their use as specific modulators of endogenous protein levels. We developed a phage-assisted continuous evolution platform for molecular glue complexes (MG-PACE) and evolved a 36-amino acid zinc finger (ZF) degron (SD40) that binds the ubiquitin ligase substrate receptor cereblon in complex with PT-179, an orthogonal thalidomide derivative. Endogenous proteins tagged in-frame with SD40 using prime editing are degraded by otherwise inert PT-179. Cryo-electron microscopy structures of SD40 in complex with ligand-bound cereblon revealed mechanistic insights into the molecular basis of SD40's activity and specificity. Our efforts establish a system for continuous evolution of molecular glue complexes and provide ZF tags that overcome shortcomings associated with existing degrons.
History
DepositionAug 2, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41424.png

Downloads & links

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Map

FileDownload / File: emd_41424.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 320 pix.
= 278.88 Å		0.87 Å/pix.
x 320 pix.
= 278.88 Å		0.87 Å/pix.
x 320 pix.
= 278.88 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8715 Å
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Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.42635822 - 0.8043359
Average (Standard dev.)0.00030143032 (±0.018418549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 278.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41424_msk_1.map
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Mask #2

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Additional map: main map, local resolution-filtered

Fileemd_41424_additional_1.map
Annotationmain map, local resolution-filtered
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Additional map: map from CRBN local refinement, post-processed with deepEMhancer

Fileemd_41424_additional_2.map
Annotationmap from CRBN local refinement, post-processed with deepEMhancer
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Additional map: main map, post-processed by deepEMhancer

Fileemd_41424_additional_3.map
Annotationmain map, post-processed by deepEMhancer
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Additional map: from local refinement with CRBN mask, half map B

Fileemd_41424_additional_4.map
Annotationfrom local refinement with CRBN mask, half map B
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Additional map: from local refinement with CRBN mask, half map A

Fileemd_41424_additional_5.map
Annotationfrom local refinement with CRBN mask, half map A
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Additional map: from local refinement with CRBN mask

Fileemd_41424_additional_6.map
Annotationfrom local refinement with CRBN mask
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Half map: half map B

Fileemd_41424_half_map_1.map
Annotationhalf map B
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Half map: half map A

Fileemd_41424_half_map_2.map
Annotationhalf map A
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Sample components

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Entire : Ternary Complex of DDB1dB:CRBN:PT-179 with SD40

EntireName: Ternary Complex of DDB1dB:CRBN:PT-179 with SD40
Components
  • Complex: Ternary Complex of DDB1dB:CRBN:PT-179 with SD40
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,SD40
  • Ligand: ZINC ION
  • Ligand: 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione

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Supramolecule #1: Ternary Complex of DDB1dB:CRBN:PT-179 with SD40

SupramoleculeName: Ternary Complex of DDB1dB:CRBN:PT-179 with SD40 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 201 KDa

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.033945 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVME LFRPKGESKD LLFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL Y DGLFKVIP ...String:
MGSSHHHHHH SAVDENLYFQ GGGRMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVME LFRPKGESKD LLFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL Y DGLFKVIP LDRDNKELKA FNIRLEELHV IDVKFLYGCQ APTICFVYQD PQGRHVKTYE VSLREKEFNK GPWKQENVEA EA SMVIAVP EPFGGAIIIG QESITYHNGD KYLAIAPPII KQSTIVCHNR VDPNGSRYLL GDMEGRLFML LLEKEEQMDG TVT LKDLRV ELLGETSIAE CLTYLDNGVV FVGSRLGDSQ LVKLNVDSNE QGSYVVAMET FTNLGPIVDM CVVDLERQGQ GQLV TCSGA FKEGSLRIIR NGIGGNGNSG EIQKLHIRTV PLYESPRKIC YQEVSQCFGV LSSRIEVQDT SGGTTALRPS ASTQA LSSS VSSSKLFSSS TAPHETSFGE EVEVHNLLII DQHTFEVLHA HQFLQNEYAL SLVSCKLGKD PNTYFIVGTA MVYPEE AEP KQGRIVVFQY SDGKLQTVAE KEVKGAVYSM VEFNGKLLAS INSTVRLYEW TTEKELRTEC NHYNNIMALY LKTKGDF IL VGDLMRSVLL LAYKPMEGNF EEIARDFNPN WMSAVEILDD DNFLGAENAF NLFVCQKDSA ATTDEERQHL QEVGLFHL G EFVNVFCHGS LVMQNLGETS TPTQGSVLFG TVNGMIGLVT SLSESWYNLL LDMQNRLNKV IKSVGKIEHS FWRSFHTER KTEPATGFID GDLIESFLDI SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH

UniProtKB: DNA damage-binding protein 1, DNA damage-binding protein 1

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Macromolecule #2: Protein cereblon

MacromoleculeName: Protein cereblon / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.144594 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDYKDDDDKS AVDENLYFQG GGRGGSAHIV MVDAYKPTKG GSGMAGEGDQ QDAAHNMGNH LPLLPAESEE EDEMEVEDQD SKEAKKPNI INFDTSLPTS HTYLGADMEE FHGRTLHDDD SCQVIPVLPQ VMMILIPGQT LPLQLFHPQE VSMVRNLIQK D RTFAVLAY ...String:
MDYKDDDDKS AVDENLYFQG GGRGGSAHIV MVDAYKPTKG GSGMAGEGDQ QDAAHNMGNH LPLLPAESEE EDEMEVEDQD SKEAKKPNI INFDTSLPTS HTYLGADMEE FHGRTLHDDD SCQVIPVLPQ VMMILIPGQT LPLQLFHPQE VSMVRNLIQK D RTFAVLAY SNVQEREAQF GTTAEIYAYR EEQDFGIEIV KVKAIGRQRF KVLELRTQSD GIQQAKVQIL PECVLPSTMS AV QLESLNK CQIFPSKPVS REDQCSYKWW QKYQKRKFHC ANLTSWPRWL YSLYDAETLM DRIKKQLREW DENLKDDSLP SNP IDFSYR VAACLPIDDV LRIQLLKIGS AIQRLRCELD IMNKCTSLCC KQCQETEITT KNEIFSLSLC GPMAAYVNPH GYVH ETLTV YKACNLNLIG RPSTEHSWFP GYAWTVAQCK ICASHIGWKF TATKKDMSPQ KFWGLTRSAL LPTIPDTEDE ISPDK VILC L

UniProtKB: Protein cereblon

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Macromolecule #3: Maltose/maltodextrin-binding periplasmic protein,SD40

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,SD40 / type: protein_or_peptide / ID: 3
Details: IZKF1/ZFP91 fusion construct that was further engineered to enhance binding of cereblon/DDB1 in the presence of IMiD derivatives
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.466012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGLNDIFEAQ KIEWHEGSSH HHHHHGSSKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIF WAHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE I PALDKELK ...String:
MGLNDIFEAQ KIEWHEGSSH HHHHHGSSKI EEGKLVIWIN GDKGYNGLAE VGKKFEKDTG IKVTVEHPDK LEEKFPQVAA TGDGPDIIF WAHDRFGGYA QSGLLAEITP DKAFQDKLYP FTWDAVRYNG KLIAYPIAVE ALSLIYNKDL LPNPPKTWEE I PALDKELK AKGKSALMFN LQEPYFTWPL IAADGGYAFK YENGKYDIKD VGVDNAGAKA GLTFLVDLIK NKHMNADTDY SI AEAAFNK GETAMTINGP WAWSNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENYLLTDEG LEA VNKDKP LGAVALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQTRI TKLE VLFQG PDYKDDDDKS GGGGLLLFCP ICGFTCRQKG NLLRHINLHT GEKLFKYHLY

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, DNA-binding protein Ikaros

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-...

MacromoleculeName: 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione
type: ligand / ID: 5 / Number of copies: 1 / Formula: MIQ
Molecular weightTheoretical: 343.334 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2625 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
3.0 mMC9H15O6PTCEP

Details: 20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
Details: Grids (Quantifoil UltrAuFoil R 1.2/1.3) were glow discharged in PELCO easiGlow (20 mA, 120s, 39 Pa)
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: LEICA EM GP
Details: Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute ...Details: Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C..
DetailsDDB1dB_CRBN, PT-179, and SD40 were mixed and incubated on ice for 1 hour at final concentration of 10.5, 105, and 21 uM, respectively. Then diluted 10-fold before blotting.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 16340 / Average exposure time: 2.497 sec. / Average electron dose: 52.0 e/Å2
Details: Movies (50 frames) collected using beam-shift with 9 holes per stage position (3x3 pattern)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6798113
Startup modelType of model: OTHER / Details: ab initio in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.0) / Number images used: 289691
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final 3D classificationNumber classes: 10 / Avg.num./class: 169059 / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8g46

chain_id: A, source_name: PDB, initial_model_type: experimental model

5fqd

chain_id: B, source_name: PDB, initial_model_type: experimental model

6h0f

chain_id: C, source_name: PDB, initial_model_type: experimental model
DetailsPhenix real-space refinement without rigid body, with ADP.
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 70 / Target criteria: Cross-correlation coefficient
Output model

PDB-8tnq:
Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1

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