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- EMDB-70865: DDB1-CRBN with ikaros(ZF2) and DEG47- consensus map submission -

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Basic information

Entry
Database: EMDB / ID: EMD-70865
TitleDDB1-CRBN with ikaros(ZF2) and DEG47- consensus map submission
Map data
Sample
  • Complex: DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was incubauted for 30 minutes and then plunge frozen over 1.2/1.3 UltrAufoil
    • Protein or peptide: DNA damage binding protein 1 (DDB1)
    • Protein or peptide: Cereblon (CRBN)
    • Protein or peptide: Ikaros (ZF2-3)
KeywordsE3 ligases / Cullin RING Ligase / CRL4 / Cereblon / CRBN / molecular glues / IMiDs / LIGASE / Ikaros
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 / mesoderm development / 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 / pericentric heterochromatin / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / erythrocyte differentiation / 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 / 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 / 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 / zinc finger / 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
DNA-binding protein Ikaros / DNA damage-binding protein 1 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 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 28, 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_70865.png

Downloads & links

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Map

FileDownload / File: emd_70865.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.228
Minimum - Maximum-1.3424541 - 1.800655
Average (Standard dev.)-0.0003451222 (±0.040197913)
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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Mask #1

Fileemd_70865_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: #1

Fileemd_70865_additional_1.map
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Histogram (log scale)

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Half map: #1

Fileemd_70865_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_70865_half_map_2.map
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Sample components

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Entire : DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was i...

EntireName: DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was incubauted for 30 minutes and then plunge frozen over 1.2/1.3 UltrAufoil
Components
  • Complex: DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was incubauted for 30 minutes and then plunge frozen over 1.2/1.3 UltrAufoil
    • Protein or peptide: DNA damage binding protein 1 (DDB1)
    • Protein or peptide: Cereblon (CRBN)
    • Protein or peptide: Ikaros (ZF2-3)

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Supramolecule #1: DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was i...

SupramoleculeName: DDB1(BPB deleted)-CRBN complex with ikaros ZF2-3 and DEG-47 was incubauted for 30 minutes and then plunge frozen over 1.2/1.3 UltrAufoil
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 151.27264 KDa

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Macromolecule #1: DNA damage binding protein 1 (DDB1)

MacromoleculeName: DNA damage binding protein 1 (DDB1) / type: protein_or_peptide / ID: 1
Details: The BPB domain is truncated (396-705 truncation with addition of a GNGNSG linker between BPA and BPC) from DDB1 and co-expressed with Cereblon (CRBN) in SF9 expression system.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL ...String:
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL YGCQAPTICF VYQDPQGRHV KTYEVSLREK EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH NGDKYLAIAP PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL RVELLGETSI AECLTYLDNG VVFVGSRLGD SQLVKLNVDS NEQGSYVVAM ETFTNLGPIV DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGGNGNS GEIQKLHIRT VPLYESPRKI CYQEVSQCFG VLSSRIEVQD TSGGTTALRP SASTQALSSS VSSSKLFSSS TAPHETSFGE EVEVHNLLII DQHTFEVLHA HQFLQNEYAL SLVSCKLGKD PNTYFIVGTA MVYPEEAEPK QGRIVVFQYS DGKLQTVAEK EVKGAVYSMV EFNGKLLASI NSTVRLYEWT TEKELRTECN HYNNIMALYL KTKGDFILVG DLMRSVLLLA YKPMEGNFEE IARDFNPNWM SAVEILDDDN FLGAENAFNL FVCQKDSAAT TDEERQHLQE VGLFHLGEFV NVFCHGSLVM QNLGETSTPT QGSVLFGTVN GMIGLVTSLS ESWYNLLLDM QNRLNKVIKS VGKIEHSFWR SFHTERKTEP ATGFIDGDLI ESFLDISRPK MQEVVANLQY DDGSGMKREA TADDLIKVVE ELTRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #2: Cereblon (CRBN)

MacromoleculeName: Cereblon (CRBN) / type: protein_or_peptide / ID: 2 / Details: 6X His tag at N-terminus / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MHHHHHHMAG EGDQQDAAHN MGNHLPLLPA ESEEEDEMEV EDQDSKEAKK PNIINFDTSL PTSHTYLGAD MEEFHGRTLH DDDSCQVIPV LPQVMMILIP GQTLPLQLFH PQEVSMVRNL IQKDRTFAVL AYSNVQEREA QFGTTAEIYA YREEQDFGIE IVKVKAIGRQ ...String:
MHHHHHHMAG EGDQQDAAHN MGNHLPLLPA ESEEEDEMEV EDQDSKEAKK PNIINFDTSL PTSHTYLGAD MEEFHGRTLH DDDSCQVIPV LPQVMMILIP GQTLPLQLFH PQEVSMVRNL IQKDRTFAVL AYSNVQEREA QFGTTAEIYA YREEQDFGIE IVKVKAIGRQ RFKVLELRTQ SDGIQQAKVQ ILPECVLPST MSAVQLESLN KCQIFPSKPV SREDQCSYKW WQKYQKRKFH CANLTSWPRW LYSLYDAETL MDRIKKQLRE WDENLKDDSL PSNPIDFSYR VAACLPIDDV LRIQLLKIGS AIQRLRCELD IMNKCTSLCC KQCQETEITT KNEIFSLSLC GPMAAYVNPH GYVHETLTVY KACNLNLIGR PSTEHSWFPG YAWTVAQCKI CASHIGWKFT ATKKDMSPQK FWGLTRSALL PTIPDTEDEI SPDKVILCL

UniProtKB: Protein cereblon

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Macromolecule #3: Ikaros (ZF2-3)

MacromoleculeName: Ikaros (ZF2-3) / type: protein_or_peptide / ID: 3 / Details: tag less / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
TGERPFQCNQ CGASFTQKGN LLRHIKLHSG EKPFKCHLCN YACRRRDALT GHLRTHS

UniProtKB: DNA-binding protein Ikaros

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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 with ikaros ZF2-3 was incubated with IMiD DEG-47 and was incubated at 1:2:13 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: 1 / Number real images: 4915 / 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: 19000
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: 3488921
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: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 412326
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 / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8d7z

chain_id: A, residue_range: 1-1148, source_name: PDB, initial_model_type: experimental model396-705 residues are truncated in construct as well as structure sequence.

8d7z

chain_id: B, residue_range: 46-427, source_name: PDB, initial_model_type: experimental model1-46 residues are not observed in EM density

8d7z

chain_id: C, residue_range: 144-169, source_name: PDB, initial_model_type: experimental model140-144 and 170-196 residues are not observed in the EM density but they were in construct.
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 97.8

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