+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8ajm | ||||||
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タイトル | Structure of human DDB1-DCAF12 in complex with the C-terminus of CCT5 | ||||||
要素 |
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キーワード | LIGASE / ubiquitin / E3 / TRiC / chaperonin | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / BBSome-mediated cargo-targeting to cilium / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / 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 / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / epigenetic programming in the zygotic pronuclei ...positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / BBSome-mediated cargo-targeting to cilium / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / 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 / 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 / chaperonin-containing T-complex / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / 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 / 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 / proteasomal protein catabolic process / 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 / 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 / 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 / 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 / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / cell body / 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 / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.83 Å | ||||||
データ登録者 | Pla-Prats, C. / Cavadini, S. / Kempf, G. / Thoma, N.H. | ||||||
資金援助 | European Union, 1件
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引用 | ジャーナル: EMBO J / 年: 2023 タイトル: Recognition of the CCT5 di-Glu degron by CRL4 is dependent on TRiC assembly. 著者: Carlos Pla-Prats / Simone Cavadini / Georg Kempf / Nicolas H Thomä / 要旨: 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. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8ajm.cif.gz | 322.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8ajm.ent.gz | 244.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8ajm.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8ajm_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8ajm_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | 8ajm_validation.xml.gz | 47.4 KB | 表示 | |
CIF形式データ | 8ajm_validation.cif.gz | 72.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/aj/8ajm ftp://data.pdbj.org/pub/pdb/validation_reports/aj/8ajm | HTTPS FTP |
-関連構造データ
関連構造データ | 15484MC 8ajnC 8ajoC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 129784.258 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DDB1, XAP1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q16531 |
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#2: タンパク質 | 分子量: 53373.191 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DCAF12, KIAA1892, TCC52, WDR40A / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q5T6F0 |
#3: タンパク質 | 分子量: 62436.809 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CCT5, CCTE, KIAA0098 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P48643 |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Complex of DDB1-DCAF12-CCT5 / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Trichoplusia ni (イラクサキンウワバ) |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 電子線照射量: 51.8 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア |
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.83 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 451315 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 169.1 Å2 | ||||||||||||||||||||||||||||||
拘束条件 |
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