Entry | Database: PDB / ID: 6xk9 |
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Title | Cereblon in complex with DDB1, CC-90009, and GSPT1 |
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Components | - DNA damage-binding protein 1
- Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
- Protein cereblon
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Keywords | LIGASE / DDB1 / molecular glue / degradation / CC-90009 / Acute Myeloid Leukemia |
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Function / homology | Function and homology information
translation release factor complex / negative regulation of monoatomic ion transmembrane transport / translation release factor activity / regulation of translational termination / positive regulation by virus of viral protein levels in host cell / protein methylation / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair ...translation release factor complex / negative regulation of monoatomic ion transmembrane transport / translation release factor activity / regulation of translational termination / positive regulation by virus of viral protein levels in host cell / protein methylation / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / Eukaryotic Translation Termination / viral release from host cell / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / proteasomal protein catabolic process / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / translational termination / positive regulation of gluconeogenesis / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / positive regulation of protein-containing complex assembly / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / G1/S transition of mitotic cell cycle / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / Potential therapeutics for SARS / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / translation / DNA repair / GTPase activity / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / GTP binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosolSimilarity search - Function Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Translation elongation factor EFTu/EF1A, C-terminal ...Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / PUA-like superfamily / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolaseSimilarity search - Domain/homology Chem-V4M / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A / DNA damage-binding protein 1 / Protein cereblonSimilarity search - Component |
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Biological species | Homo sapiens (human) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.64 Å |
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Authors | Clayton, T.L. / Tran, E.T. / Zhu, J. / Pagarigan, B.E. / Matyskiela, M.E. / Chamberlain, P.P. |
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Citation | Journal: Blood / Year: 2021 Title: CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells. Authors: Surka, C. / Jin, L. / Mbong, N. / Lu, C.C. / Jang, I.S. / Rychak, E. / Mendy, D. / Clayton, T. / Tindall, E. / Hsu, C. / Fontanillo, C. / Tran, E. / Contreras, A. / Ng, S.W.K. / Matyskiela, ...Authors: Surka, C. / Jin, L. / Mbong, N. / Lu, C.C. / Jang, I.S. / Rychak, E. / Mendy, D. / Clayton, T. / Tindall, E. / Hsu, C. / Fontanillo, C. / Tran, E. / Contreras, A. / Ng, S.W.K. / Matyskiela, M. / Wang, K. / Chamberlain, P. / Cathers, B. / Carmichael, J. / Hansen, J. / Wang, J.C.Y. / Minden, M.D. / Fan, J. / Pierce, D.W. / Pourdehnad, M. / Rolfe, M. / Lopez-Girona, A. / Dick, J.E. / Lu, G. |
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History | Deposition | Jun 25, 2020 | Deposition site: RCSB / Processing site: RCSB |
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Revision 1.0 | Dec 2, 2020 | Provider: repository / Type: Initial release |
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Revision 1.1 | Feb 24, 2021 | Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name |
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Revision 1.2 | Oct 18, 2023 | Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id |
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