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- EMDB-70862: DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map an... -

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Basic information

Entry
Database: EMDB / ID: EMD-70862
TitleDDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission
Map data
Sample
  • Complex: DDB1(BPB deleted)-CRBN complex with Casein kinase 1 alpha, SB-405483, and DEG-47
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Casein kinase I isoform alpha
  • Ligand: ZINC ION
  • Ligand: N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide
  • Ligand: N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea
KeywordsE3 ligases / Cullin RING Ligase / CRL4 / Cereblon / CRBN / molecular glues / IMiDs / LIGASE
Function / homology
Function and homology information


intermediate filament cytoskeleton organization / negative regulation of monoatomic ion transmembrane transport / Activation of SMO / negative regulation of NLRP3 inflammasome complex assembly / cellular response to nutrient / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation by virus of viral protein levels in host cell ...intermediate filament cytoskeleton organization / negative regulation of monoatomic ion transmembrane transport / Activation of SMO / negative regulation of NLRP3 inflammasome complex assembly / cellular response to nutrient / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation by virus of viral protein levels in host cell / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / 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 / positive regulation of Rho protein signal transduction / Golgi organization / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of TORC1 signaling / positive regulation of gluconeogenesis / nucleotide-excision repair / positive regulation of protein-containing complex assembly / Recognition of DNA damage by PCNA-containing replication complex / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / DNA Damage Recognition in GG-NER / kinetochore / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / spindle / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / 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 / chromosome, telomeric region / cell surface receptor signaling pathway / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / viral protein processing / nuclear speck / protein ubiquitination / cilium / ciliary basal body / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / apoptotic process / DNA damage response / centrosome / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / signal transduction / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / ATP binding
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Casein kinase I isoform alpha / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsRizvi Z / Lander GC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143805 United States
CitationJournal: To Be Published
Title: Identification of a cryptic allosteric site on the E3 ligase adapter protein cereblon
Authors: Rizvi Z / Dippon VN / Choudhry AE / Chung CW / Alkuraya IF / Xu W / Tao XB / Jurewicz AJ / Schneck JL / Chen W / Curnutt NM / Kabir F / Chan KH / Queisser MA / Musetti C / Dai H / Benowitz ...Authors: Rizvi Z / Dippon VN / Choudhry AE / Chung CW / Alkuraya IF / Xu W / Tao XB / Jurewicz AJ / Schneck JL / Chen W / Curnutt NM / Kabir F / Chan KH / Queisser MA / Musetti C / Dai H / Benowitz AB / Woo CM / Lander GC
History
DepositionMay 27, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70862.png

Downloads & links

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Map

FileDownload / File: emd_70862.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0346
Minimum - Maximum-0.12864304 - 0.4951277
Average (Standard dev.)0.0015025148 (±0.011231561)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 222.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DDB1(BPB deleted)-CRBN complex with Casein kinase 1 alpha, SB-405...

EntireName: DDB1(BPB deleted)-CRBN complex with Casein kinase 1 alpha, SB-405483, and DEG-47
Components
  • Complex: DDB1(BPB deleted)-CRBN complex with Casein kinase 1 alpha, SB-405483, and DEG-47
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Protein cereblon
    • Protein or peptide: Casein kinase I isoform alpha
  • Ligand: ZINC ION
  • Ligand: N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide
  • Ligand: N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea

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Supramolecule #1: DDB1(BPB deleted)-CRBN complex with Casein kinase 1 alpha, SB-405...

SupramoleculeName: DDB1(BPB deleted)-CRBN complex with Casein kinase 1 alpha, SB-405483, and DEG-47
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: The protein complex was incubated with CK1a, IMiD DEG-47, and allosteric binder SB-405483, and the mixture was incubated at 1:2:13:20 for 30 minutes and then frozen on 1.2/1.3 Au grids
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 183.66303 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: 93.061852 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...String:
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRLHIRT VPLY ESPRK ICYQEVSQCF GVLSSRIEVQ DTSGGTTALR PSASTQALSS SVSSSKLFSS STAPHETSFG EEVEVHNLLI IDQHT FEVL HAHQFLQNEY ALSLVSCKLG KDPNTYFIVG TAMVYPEEAE PKQGRIVVFQ YSDGKLQTVA EKEVKGAVYS MVEFNG KLL ASINSTVRLY EWTTEKELRT ECNHYNNIMA LYLKTKGDFI LVGDLMRSVL LLAYKPMEGN FEEIARDFNP NWMSAVE IL DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL GEFVNVFCHG SLVMQNLGET STPTQGSVLF GTVNGMIG L VTSLSESWYN LLLDMQNRLN KVIKSVGKIE HSFWRSFHTE RKTEPATGFI DGDLIESFLD ISRPKMQEVV ANLQYDDGS GMKREATADD LIKVVEELTR IHWSHPQFEK

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: 43.978617 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: IINFDTSLPT SHTYLGADME EFHGRTLHDD DSCQVIPVLP QVMMILIPGQ TLPLQLFHPQ EVSMVRNLIQ KDRTFAVLAY SNVQEREAQ FGTTAEIYAY REEQDFGIEI VKVKAIGRQR FKVLELRTQS DGIQQAKVQI LPECVLPSTM SAVQLESLNK C QIFPSKPV ...String:
IINFDTSLPT SHTYLGADME EFHGRTLHDD DSCQVIPVLP QVMMILIPGQ TLPLQLFHPQ EVSMVRNLIQ KDRTFAVLAY SNVQEREAQ FGTTAEIYAY REEQDFGIEI VKVKAIGRQR FKVLELRTQS DGIQQAKVQI LPECVLPSTM SAVQLESLNK C QIFPSKPV SREDQCSYKW WQKYQKRKFH CANLTSWPRW LYSLYDAETL MDRIKKQLRE WDENLKDDSL PSNPIDFSYR VA ACLPIDD VLRIQLLKIG SAIQRLRCEL DIMNKCTSLC CKQCQETEIT TKNEIFSLSL CGPMAAYVNP HGYVHETLTV YKA CNLNLI GRPSTEHSWF PGYAWTVAQC KICASHIGWK FTATKKDMSP QKFWGLTRSA LLPTIP

UniProtKB: Protein cereblon

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Macromolecule #3: Casein kinase I isoform alpha

MacromoleculeName: Casein kinase I isoform alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.682211 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: EFIVGGKYKL VRKIGSGSFG DIYLAINITN GEEVAVKLES QKARHPQLLY ESKLYKILQG GVGIPHIRWY GQEKDYNVLV MDLLGPSLE DLFNFCSRRF TMKTVLMLAD QMISRIEYVH TKNFIHRDIK PDNFLMGIGR HCNKLFLIDF GLAKKYRDNR T RQHIPYRE ...String:
EFIVGGKYKL VRKIGSGSFG DIYLAINITN GEEVAVKLES QKARHPQLLY ESKLYKILQG GVGIPHIRWY GQEKDYNVLV MDLLGPSLE DLFNFCSRRF TMKTVLMLAD QMISRIEYVH TKNFIHRDIK PDNFLMGIGR HCNKLFLIDF GLAKKYRDNR T RQHIPYRE DKNLTGTARY ASINAHLGIE QSRRDDMESL GYVLMYFNRT SLPWQGLKAA TKKQKYEKIS EKKMSTPVEV LC KGFPAEF AMYLNYCRGL RFEEAPDYMY LRQLFRILFR TLNHQYDYTF DWTMLKQ

UniProtKB: Casein kinase I isoform alpha

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol...

MacromoleculeName: N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1CEH
Molecular weightTheoretical: 363.367 Da

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Macromolecule #6: N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea

MacromoleculeName: N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1CEG
Molecular weightTheoretical: 360.366 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

Concentration0.5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
240.0 mMNaClSodium Chloride
3.0 mMC9H15O6PTCEP

Details: 10mM HEPES, 240mM NaCl, 3mM TCEP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 100.1 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 12 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.0239980266 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER
DetailsThe protein complex was incubated with CK1a, IMiD DEG-47, and allosteric binder SB-405483, and the mixture was incubated at 1:2:13:20 for 30 minutes and then frozen on 1.2/1.3 Au grids

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMin: 70.0 K / Max: 77.0 K
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 5691 / Average exposure time: 4.08 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 189189 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3492611
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL / In silico model: AB INITIO RECONSTRUCTION
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 328293
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Details: Ab initio reconstruction, heterogeneous refinement, and homogeneous refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2) / Details: Non uniform refinement
Final 3D classificationNumber classes: 6

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
chain_id: A, residue_range: 1-1148, source_name: Other, initial_model_type: experimental modelThe initial model was coming from crystal structure model from this study mentioned in citation
chain_id: B, residue_range: 46-427, source_name: Other, initial_model_type: experimental modelThe initial model was coming from crystal structure model from this study mentioned in citation
chain_id: C, residue_range: 10-299, source_name: PDB, initial_model_type: experimental modelCK1a model was taken from published structure 5fqd

5fqd

RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 102.6
Output model

PDB-9oty:
DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission

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