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- EMDB-15484: Structure of human DDB1-DCAF12 in complex with the C-terminus of CCT5 -

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Basic information

Entry
Database: EMDB / ID: EMD-15484
TitleStructure of human DDB1-DCAF12 in complex with the C-terminus of CCT5
Map dataLocally sharpened map (LocScale).
Sample
  • Complex: Complex of DDB1-DCAF12-CCT5
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 12
    • Protein or peptide: T-complex protein 1 subunit epsilon
Function / homology
Function and homology information


positive regulation of protein localization to Cajal body / positive regulation of establishment of protein localization to telomere / BBSome-mediated cargo-targeting to cilium / chaperonin-containing T-complex / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / positive regulation by virus of viral protein levels in host cell / binding of sperm to zona pellucida / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway ...positive regulation of protein localization to Cajal body / positive regulation of establishment of protein localization to telomere / BBSome-mediated cargo-targeting to cilium / chaperonin-containing T-complex / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / positive regulation by virus of viral protein levels in host cell / binding of sperm to zona pellucida / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / 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 / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / beta-tubulin binding / negative regulation of reproductive process / negative regulation of developmental process / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / chaperone-mediated protein folding / protein folding chaperone / positive regulation of gluconeogenesis / positive regulation of telomere maintenance via telomerase / T cell activation / regulation of autophagy / mRNA 3'-UTR binding / proteasomal protein catabolic process / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / ATP-dependent protein folding chaperone / DNA Damage Recognition in GG-NER / response to virus / mRNA 5'-UTR binding / 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 / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / positive regulation of protein catabolic process / G-protein beta-subunit binding / cellular response to UV / rhythmic process / unfolded protein binding / protein-macromolecule adaptor activity / protein folding / site of double-strand break / cell body / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / chromosome, telomeric region / damaged DNA binding / protein stabilization / protein ubiquitination / DNA repair / centrosome / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / ATP hydrolysis activity / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
T-complex protein 1, epsilon subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / 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 ...T-complex protein 1, epsilon subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / 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 / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
T-complex protein 1 subunit epsilon / DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsPla-Prats C / Cavadini S / Kempf G / Thoma NH
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: 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
DepositionJul 28, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15484.png

Downloads & links

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Map

FileDownload / File: emd_15484.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally sharpened map (LocScale).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å		0.86 Å/pix.
x 280 pix.
= 240.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.33868563 - 0.877353
Average (Standard dev.)0.002293241 (±0.022302153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 240.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full map.

Fileemd_15484_additional_1.map
AnnotationFull map.
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15484_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15484_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of DDB1-DCAF12-CCT5

EntireName: Complex of DDB1-DCAF12-CCT5
Components
  • Complex: Complex of DDB1-DCAF12-CCT5
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DDB1- and CUL4-associated factor 12
    • Protein or peptide: T-complex protein 1 subunit epsilon

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Supramolecule #1: Complex of DDB1-DCAF12-CCT5

SupramoleculeName: Complex of DDB1-DCAF12-CCT5 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.784258 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #2: DDB1- and CUL4-associated factor 12

MacromoleculeName: DDB1- and CUL4-associated factor 12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.373191 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #3: T-complex protein 1 subunit epsilon

MacromoleculeName: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.436809 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 451315

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