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- PDB-9v0b: Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2... -

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Basic information

Entry
Database: PDB / ID: 9v0b
TitleCryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
Components
  • Cullin-4A
  • DNA damage-binding protein 1
  • E3 ubiquitin-protein ligase RBX1, N-terminally processed
  • NEDD8
  • Protein cereblon
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 D1
  • Zinc finger protein Aiolos
KeywordsLIGASE / Molecular glue degrader / avadomide / CRL4 ubiquitin ligase / DDB1 / CRBN / Complex
Function / homology
Function and homology information


regulation of lymphocyte differentiation / regulation of B cell differentiation / regulation of B cell proliferation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / nucleotide-excision repair complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Phosphorylation of the APC/C / cellular response to camptothecin ...regulation of lymphocyte differentiation / regulation of B cell differentiation / regulation of B cell proliferation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / nucleotide-excision repair complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Phosphorylation of the APC/C / cellular response to camptothecin / negative regulation of monoatomic ion transmembrane transport / Signaling by BMP / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING ubiquitin ligase complex / negative regulation of mitophagy / regulation of xenophagy / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation by virus of viral protein levels in host cell / positive regulation of protein autoubiquitination / protein neddylation / regulation of BMP signaling pathway / NEDD8 ligase activity / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / protein K27-linked ubiquitination / UV-damage excision repair / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / E2 ubiquitin-conjugating enzyme / regulation of TOR signaling / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / biological process involved in interaction with symbiont / SCF ubiquitin ligase complex / regulation of mitotic cytokinesis / regulation of DNA damage checkpoint / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / mesoderm development / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / WD40-repeat domain binding / Prolactin receptor signaling / Formation of the ternary complex, and subsequently, the 43S complex / regulation of cell cycle phase transition / locomotory exploration behavior / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Regulation of APC/C activators between G1/S and early anaphase / Cul4A-RING E3 ubiquitin ligase complex / Ribosomal scanning and start codon recognition / TGF-beta receptor signaling activates SMADs / negative regulation of BMP signaling pathway / Cul4B-RING E3 ubiquitin ligase complex / Translation initiation complex formation / ubiquitin ligase complex scaffold activity / Transcriptional Regulation by VENTX / negative regulation of adipose tissue development / ubiquitin conjugating enzyme activity / T cell differentiation / regulation of proteolysis / regulation of cellular response to stress / limb development / viral release from host cell / regulation of postsynapse assembly / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SARS-CoV-1 modulates host translation machinery / protein monoubiquitination / Peptide chain elongation / anatomical structure morphogenesis / cullin family protein binding / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / positive regulation of Wnt signaling pathway / Viral mRNA Translation / negative regulation of protein-containing complex assembly / centrosome duplication / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / regulation of DNA-templated DNA replication initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / positive regulation of viral genome replication / cilium assembly
Similarity search - Function
: / Nedd8-like ubiquitin / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain ...: / Nedd8-like ubiquitin / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / 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) / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / : / 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 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / PUA-like superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Zinc finger, C2H2 type / Ubiquitin-conjugating enzyme/RWD-like / zinc finger / Zinc finger C2H2 type domain profile. / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-835 / Ubiquitin-conjugating enzyme E2 D1 / E3 ubiquitin-protein ligase RBX1 / Ubiquitin-ribosomal protein eS31 fusion protein / Cullin-4A / Ubiquitin-like protein NEDD8 / DNA damage-binding protein 1 / Protein cereblon / Zinc finger protein Aiolos
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsDeng, Z.H. / Ai, H.S. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810, T2488301 China
CitationJournal: To Be Published
Title: Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
Authors: Deng, Z.H. / Ai, H.S. / Liu, L.
History
DepositionMay 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data 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: Cullin-4A
B: DNA damage-binding protein 1
C: Protein cereblon
D: Ubiquitin-conjugating enzyme E2 D1
I: Zinc finger protein Aiolos
N: NEDD8
R: E3 ubiquitin-protein ligase RBX1, N-terminally processed
U: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,66815
Polymers317,9898
Non-polymers6797
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 , 8 types, 8 molecules ABCDINRU

#1: Protein Cullin-4A / CUL-4A


Mass: 89368.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL4A / Production host: Escherichia coli (E. coli) / References: UniProt: Q13619
#2: 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: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Homo sapiens (human) / References: UniProt: Q16531
#3: Protein Protein cereblon


Mass: 48874.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Homo sapiens (human) / References: UniProt: Q96SW2
#4: Protein Ubiquitin-conjugating enzyme E2 D1 / (E3-independent) E2 ubiquitin-conjugating enzyme D1 / E2 ubiquitin-conjugating enzyme D1 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D1 / E2 ubiquitin-conjugating enzyme D1 / Stimulator of Fe transport / SFT / UBC4/5 homolog / UbcH5 / Ubiquitin carrier protein D1 / Ubiquitin-conjugating enzyme E2(17)KB 1 / Ubiquitin-conjugating enzyme E2-17 kDa 1 / Ubiquitin-protein ligase D1


Mass: 16490.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A / Production host: Escherichia coli (E. coli)
References: UniProt: P51668, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#5: Protein Zinc finger protein Aiolos / Ikaros family zinc finger protein 3


Mass: 6549.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKZF3, ZNFN1A3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKT9
#6: Protein NEDD8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 8573.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843
#7: Protein E3 ubiquitin-protein ligase RBX1, N-terminally processed / E3 ubiquitin-protein transferase RBX1 / N-terminally processed


Mass: 12457.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62877
#8: Protein Ubiquitin / Donor Ub


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62979

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Non-polymers , 2 types, 7 molecules

#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-835 / (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione / (3S)-3-(5-amino-2-methyl-4-oxoquinazolin-3-yl)piperidine-2,6-dione


Mass: 286.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N4O3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: Avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
31Homo sapiens (human)9606
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1.1particle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC4.7.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60674 / Symmetry type: POINT
RefinementHighest resolution: 3.54 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421138
ELECTRON MICROSCOPYf_angle_d0.63128596
ELECTRON MICROSCOPYf_dihedral_angle_d4.6962820
ELECTRON MICROSCOPYf_chiral_restr0.0453231
ELECTRON MICROSCOPYf_plane_restr0.0043668

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