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

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Basic information

Entry
Database: PDB / ID: 9oty
TitleDDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission
Components
  • Casein kinase I isoform alpha
  • DNA damage-binding protein 1
  • Protein cereblon
KeywordsLIGASE / E3 ligases / Cullin RING Ligase / CRL4 / Cereblon / CRBN / molecular glues / IMiDs
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 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / UV-damage excision repair / 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 / viral release from host cell / cullin family protein binding / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / positive regulation of viral genome replication / negative regulation of protein-containing complex assembly / proteasomal protein catabolic process / positive regulation of TORC1 signaling / positive regulation of gluconeogenesis / nucleotide-excision repair / positive regulation of protein-containing complex assembly / negative regulation of canonical Wnt signaling pathway / Recognition of DNA damage by PCNA-containing replication complex / 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 / 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 / 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 / cilium / protein ubiquitination / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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: Nature / Year: 2025
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, A.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, A.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 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.1Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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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: Casein kinase I isoform alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,5126
Polymers171,7233
Non-polymers7893
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules ABC

#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: 93061.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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: 43978.617 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 Casein kinase I isoform alpha / CKI-alpha / CK1


Mass: 34682.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1A1 / Plasmid: pFASTBac / Cell line (production host): Sf9
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P48729, non-specific serine/threonine protein kinase

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1CEH / N-{2-[(3R)-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
#6: Chemical ChemComp-A1CEG / N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea


Mass: 360.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16N4O3 / Feature type: SUBJECT OF INVESTIGATION

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Details

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 Casein kinase 1 alpha, SB-405483, and DEG-47
Type: COMPLEX
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
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.18366303 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Strain: Sf9 / 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 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
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: 190000 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: 2 / Num. of real images: 5691
Image scansSampling size: 15 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
4cryoSPARC4.6.2CTF correction
7Coot0.9.8.95 ELmodel fitting
9cryoSPARC4.6.2initial Euler assignment
10cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.23D reconstruction
13PHENIXv2.0orc1-5617model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 3492611
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 328293 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 102.6 / Protocol: RIGID BODY FIT / Space: RECIPROCAL
Atomic model building

3D fitting-ID: 1 / Type: experimental model

IDPDB-IDPdb chain-IDChain-IDChain residue rangeDetailsSource nameAccession codeInitial refinement model-IDPdb chain residue range
1A1-1148The initial model was coming from crystal structure model from this study mentioned in citationOther
2B46-427The initial model was coming from crystal structure model from this study mentioned in citationOther
35fqd

5fqd

CC10-299CK1a model was taken from published structure 5fqdPDB5fqd210-299
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411774
ELECTRON MICROSCOPYf_angle_d0.76915904
ELECTRON MICROSCOPYf_dihedral_angle_d12.0584383
ELECTRON MICROSCOPYf_chiral_restr0.0521773
ELECTRON MICROSCOPYf_plane_restr0.0052026

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