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- PDB-9ouk: DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model su... -

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Basic information

Entry
Database: PDB / ID: 9ouk
TitleDDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission
Components
  • DNA damage-binding protein 1
  • DNA-binding protein Ikaros
  • Protein cereblon
KeywordsLIGASE / E3 ligases / Cullin RING Ligase / CRL4 / Cereblon / CRBN / molecular glues / IMiDs / 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 / viral release from host cell / cullin family protein binding / 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 / Wnt signaling pathway / Formation of Incision Complex in GG-NER / 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 / cytosol / cytoplasm
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsRizvi, Z. / Lander, G.C.
Funding support United States, 1items
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, V.N. / Choudhry, A.E. / Chung, C.W. / Alkuraya, I.F. / Xu, W. / Tao, X.B. / Jurewicz, A.J. / Schneck, J.L. / Chen, W. / Curnutt, N.M. / Kabir, F. / Chan, K.H. / Queisser, ...Authors: Rizvi, Z. / Dippon, V.N. / Choudhry, A.E. / Chung, C.W. / Alkuraya, I.F. / Xu, W. / Tao, X.B. / Jurewicz, A.J. / Schneck, J.L. / Chen, W. / Curnutt, N.M. / Kabir, F. / Chan, K.H. / Queisser, M.A. / Musetti, C. / Dai, H. / Benowitz, A.B. / Woo, C.M. / Lander, G.C.
History
DepositionMay 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA damage-binding protein 1
B: Protein cereblon
C: DNA-binding protein Ikaros
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,9876
Polymers152,4933
Non-polymers4943
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 DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 94389.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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,
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Plasmid: pFASTBac / Cell line (production host): Sf9
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q16531
#2: Protein Protein cereblon


Mass: 51563.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Plasmid: pFASTBac / Cell line (production host): Sf9
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q96SW2
#3: Protein DNA-binding protein Ikaros / Ikaros family zinc finger protein 1 / Lymphoid transcription factor LyF-1


Mass: 6539.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKZF1, IK1, IKAROS, LYF1, ZNFN1A1 / Plasmid: pet28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q13422
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-A1CEK / N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide


Mass: 363.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N3O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 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 / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.15127264 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Strain: sf9 / Cell: insect cell / Plasmid: pFASTBac
Buffer solutionpH: 7 / Details: 10mM HEPES, 240mM NaCl, 3mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESC8H18N2O4S1
2240 mMSodium ChlorideNaCl1
33 mMTCEPC9H15O6P1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The 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
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 19000 X / Calibrated magnification: 189189 X / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 70 K
Image recordingAverage exposure time: 4.08 sec. / Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4915
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2EPU3.9.1.8206image acquisition
4cryoSPARC4.6.2CTF correction
7Coot0.9.8.95 EL (ccp4)model fitting
9cryoSPARC4.6.2initial Euler assignment
10cryoSPARC4.6.2final Euler assignment
11cryoSPARC4.6.2classification
12cryoSPARC4.6.23D reconstruction
13PHENIXv2.0orc1-5617model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 3488921
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 412326 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 97.8 / Protocol: RIGID BODY FIT / Space: RECIPROCAL
Atomic model building

3D fitting-ID: 1 / Accession code: 8d7z / Initial refinement model-ID: 1 / PDB-ID: 8d7z

8d7z

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-IDChain residue rangeDetailsPdb chain residue range
1AA1-1148396-705 residues are truncated in construct as well as structure sequence.1-1148
2BB46-4271-46 residues are not observed in EM density46-427
3CC144-169140-144 and 170-196 residues are not observed in the EM density but they were in construct.144-169
RefinementHighest resolution: 2.69 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029830
ELECTRON MICROSCOPYf_angle_d0.57113297
ELECTRON MICROSCOPYf_dihedral_angle_d7.4091324
ELECTRON MICROSCOPYf_chiral_restr0.0431495
ELECTRON MICROSCOPYf_plane_restr0.0041704

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