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Yorodumi- EMDB-15486: Negative-stain electron microscopy structure of DDB1-DCAF12-CCT5 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15486 | |||||||||
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Title | Negative-stain electron microscopy structure of DDB1-DCAF12-CCT5 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | chaperone / E3 / ubiquitin / DDB1 / DCAF12 / LIGASE | |||||||||
Function / homology | Function and homology information positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / BBSome-mediated cargo-targeting to cilium / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / positive regulation by virus of viral protein levels in host cell / chaperonin-containing T-complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway ...positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / BBSome-mediated cargo-targeting to cilium / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / positive regulation by virus of viral protein levels in host cell / chaperonin-containing T-complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Prefoldin mediated transfer of substrate to CCT/TriC / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / ubiquitin-like ligase-substrate adaptor activity / proteasomal protein catabolic process / positive regulation of viral genome replication / chaperone-mediated protein folding / positive regulation of gluconeogenesis / protein folding chaperone / positive regulation of telomere maintenance via telomerase / T cell activation / regulation of autophagy / mRNA 3'-UTR binding / nucleotide-excision repair / ATP-dependent protein folding chaperone / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / response to virus / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / mRNA 5'-UTR binding / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / cellular response to UV / G-protein beta-subunit binding / unfolded protein binding / rhythmic process / protein folding / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / cell body / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / damaged DNA binding / chromosome, telomeric region / protein stabilization / protein ubiquitination / DNA repair / centrosome / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / apoptotic process / ATP hydrolysis activity / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 30.6 Å | |||||||||
Authors | Pla-Prats C / Cavadini S / Kempf G / Thoma NH | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: EMBO J / Year: 2023 Title: Recognition of the CCT5 di-Glu degron by CRL4 is dependent on TRiC assembly. Authors: Carlos Pla-Prats / Simone Cavadini / Georg Kempf / Nicolas H Thomä / Abstract: Assembly Quality Control (AQC) E3 ubiquitin ligases target incomplete or incorrectly assembled protein complexes for degradation. The CUL4-RBX1-DDB1-DCAF12 (CRL4 ) E3 ligase preferentially ...Assembly Quality Control (AQC) E3 ubiquitin ligases target incomplete or incorrectly assembled protein complexes for degradation. The CUL4-RBX1-DDB1-DCAF12 (CRL4 ) E3 ligase preferentially ubiquitinates proteins that carry a C-terminal double glutamate (di-Glu) motif. Reported CRL4 di-Glu-containing substrates include CCT5, a subunit of the TRiC chaperonin. How DCAF12 engages its substrates and the functional relationship between CRL4 and CCT5/TRiC is currently unknown. Here, we present the cryo-EM structure of the DDB1-DCAF12-CCT5 complex at 2.8 Å resolution. DCAF12 serves as a canonical WD40 DCAF substrate receptor and uses a positively charged pocket at the center of the β-propeller to bind the C-terminus of CCT5. DCAF12 specifically reads out the CCT5 di-Glu side chains, and contacts other visible degron amino acids through Van der Waals interactions. The CCT5 C-terminus is inaccessible in an assembled TRiC complex, and functional assays demonstrate that DCAF12 binds and ubiquitinates monomeric CCT5, but not CCT5 assembled into TRiC. Our biochemical and structural results suggest a previously unknown role for the CRL4 E3 ligase in overseeing the assembly of a key cellular complex. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15486.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-15486-v30.xml emd-15486.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_15486.png | 38.3 KB | ||
Filedesc metadata | emd-15486.cif.gz | 6.5 KB | ||
Others | emd_15486_half_map_1.map.gz emd_15486_half_map_2.map.gz | 29.6 MB 29.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15486 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15486 | HTTPS FTP |
-Validation report
Summary document | emd_15486_validation.pdf.gz | 539.7 KB | Display | EMDB validaton report |
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Full document | emd_15486_full_validation.pdf.gz | 539.2 KB | Display | |
Data in XML | emd_15486_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_15486_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15486 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15486 | HTTPS FTP |
-Related structure data
Related structure data | 8ajoMC 8ajmC 8ajnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15486.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.125 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15486_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15486_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of DDB1-DCAF12-CCT5
Entire | Name: Complex of DDB1-DCAF12-CCT5 |
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Components |
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-Supramolecule #1: Complex of DDB1-DCAF12-CCT5
Supramolecule | Name: Complex of DDB1-DCAF12-CCT5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: DNA damage-binding protein 1
Macromolecule | Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 129.784258 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGSSHHHHHH SAVDENLYFQ GGGRMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVME LFRPKGESKD LLFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL Y DGLFKVIP ...String: MGSSHHHHHH SAVDENLYFQ GGGRMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVME LFRPKGESKD LLFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL Y DGLFKVIP LDRDNKELKA FNIRLEELHV IDVKFLYGCQ APTICFVYQD PQGRHVKTYE VSLREKEFNK GPWKQENVEA EA SMVIAVP EPFGGAIIIG QESITYHNGD KYLAIAPPII KQSTIVCHNR VDPNGSRYLL GDMEGRLFML LLEKEEQMDG TVT LKDLRV ELLGETSIAE CLTYLDNGVV FVGSRLGDSQ LVKLNVDSNE QGSYVVAMET FTNLGPIVDM CVVDLERQGQ GQLV TCSGA FKEGSLRIIR NGIGIHEHAS IDLPGIKGLW PLRSDPNRET DDTLVLSFVG QTRVLMLNGE EVEETELMGF VDDQQ TFFC GNVAHQQLIQ ITSASVRLVS QEPKALVSEW KEPQAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEH EVA CLDITPLGDS NGLSPLCAIG LWTDISARIL KLPSFELLHK EMLGGEIIPR SILMTTFESS HYLLCALGDG ALFYFGL NI ETGLLSDRKK VTLGTQPTVL RTFRSLSTTN VFACSDRPTV IYSSNHKLVF SNVNLKEVNY MCPLNSDGYP DSLALANN S TLTIGTIDEI QKLHIRTVPL YESPRKICYQ EVSQCFGVLS SRIEVQDTSG GTTALRPSAS TQALSSSVSS SKLFSSSTA PHETSFGEEV EVHNLLIIDQ HTFEVLHAHQ FLQNEYALSL VSCKLGKDPN TYFIVGTAMV YPEEAEPKQG RIVVFQYSDG KLQTVAEKE VKGAVYSMVE FNGKLLASIN STVRLYEWTT EKELRTECNH YNNIMALYLK TKGDFILVGD LMRSVLLLAY K PMEGNFEE IARDFNPNWM SAVEILDDDN FLGAENAFNL FVCQKDSAAT TDEERQHLQE VGLFHLGEFV NVFCHGSLVM QN LGETSTP TQGSVLFGTV NGMIGLVTSL SESWYNLLLD MQNRLNKVIK SVGKIEHSFW RSFHTERKTE PATGFIDGDL IES FLDISR PKMQEVVANL QYDDGSGMKR EATADDLIKV VEELTRIH UniProtKB: DNA damage-binding protein 1 |
-Macromolecule #2: DDB1- and CUL4-associated factor 12
Macromolecule | Name: DDB1- and CUL4-associated factor 12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 53.373191 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDWSHPQFEK SAVDENLYFQ GGGRMARKVV SRKRKAPASP GAGSDAQGPQ FGWDHSLHKR KRLPPVKRSL VYYLKNREVR LQNETSYSR VLHGYAAQQL PSLLKEREFH LGTLNKVFAS QWLNHRQVVC GTKCNTLFVV DVQTSQITKI PILKDREPGG V TQQGCGIH ...String: MDWSHPQFEK SAVDENLYFQ GGGRMARKVV SRKRKAPASP GAGSDAQGPQ FGWDHSLHKR KRLPPVKRSL VYYLKNREVR LQNETSYSR VLHGYAAQQL PSLLKEREFH LGTLNKVFAS QWLNHRQVVC GTKCNTLFVV DVQTSQITKI PILKDREPGG V TQQGCGIH AIELNPSRTL LATGGDNPNS LAIYRLPTLD PVCVGDDGHK DWIFSIAWIS DTMAVSGSRD GSMGLWEVTD DV LTKSDAR HNVSRVPVYA HITHKALKDI PKEDTNPDNC KVRALAFNNK NKELGAVSLD GYFHLWKAEN TLSKLLSTKL PYC RENVCL AYGSEWSVYA VGSQAHVSFL DPRQPSYNVK SVCSRERGSG IRSVSFYEHI ITVGTGQGSL LFYDIRAQRF LEER LSACY GSKPRLAGEN LKLTTGKGWL NHDETWRNYF SDIDFFPNAV YTHCYDSSGT KLFVAGGPLP SGLHGNYAGL WS UniProtKB: DDB1- and CUL4-associated factor 12 |
-Macromolecule #3: T-complex protein 1 subunit epsilon
Macromolecule | Name: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 62.436809 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGSSHHHHHH SAVDENLYFQ GGGRMASMGT LAFDEYGRPF LIIKDQDRKS RLMGLEALKS HIMAAKAVAN TMRTSLGPNG LDKMMVDKD GDVTVTNDGA TILSMMDVDH QIAKLMVELS KSQDDEIGDG TTGVVVLAGA LLEEAEQLLD RGIHPIRIAD G YEQAARVA ...String: MGSSHHHHHH SAVDENLYFQ GGGRMASMGT LAFDEYGRPF LIIKDQDRKS RLMGLEALKS HIMAAKAVAN TMRTSLGPNG LDKMMVDKD GDVTVTNDGA TILSMMDVDH QIAKLMVELS KSQDDEIGDG TTGVVVLAGA LLEEAEQLLD RGIHPIRIAD G YEQAARVA IEHLDKISDS VLVDIKDTEP LIQTAKTTLG SKVVNSCHRQ MAEIAVNAVL TVADMERRDV DFELIKVEGK VG GRLEDTK LIKGVIVDKD FSHPQMPKKV EDAKIAILTC PFEPPKPKTK HKLDVTSVED YKALQKYEKE KFEEMIQQIK ETG ANLAIC QWGFDDEANH LLLQNNLPAV RWVGGPEIEL IAIATGGRIV PRFSELTAEK LGFAGLVQEI SFGTTKDKML VIEQ CKNSR AVTIFIRGGN KMIIEEAKRS LHDALCVIRN LIRDNRVVYG GGAAEISCAL AVSQEADKCP TLEQYAMRAF ADALE VIPM ALSENSGMNP IQTMTEVRAR QVKEMNPALG IDCLHKGTND MKQQHVIETL IGKKQQISLA TQMVRMILKI DDIRKP GES EE UniProtKB: T-complex protein 1 subunit epsilon |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Staining | Type: NEGATIVE / Material: Uranyl acetate |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 200.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 30.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2923 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |