+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8f0u | ||||||
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タイトル | Structure of a 12mer DegP cage bound to the client protein hTRF1 | ||||||
要素 |
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キーワード | CHAPERONE / HYDROLASE / Protease / cage / complex | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / peptidase Do / t-circle formation ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / peptidase Do / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / telomere capping / Telomere C-strand (Lagging Strand) Synthesis / : / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / chaperone-mediated protein folding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere maintenance / Meiotic synapsis / serine-type peptidase activity / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / spindle / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / microtubule binding / response to oxidative stress / chromosome, telomeric region / periplasmic space / nuclear body / cell division / serine-type endopeptidase activity / nucleolus / protein homodimerization activity / proteolysis / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Escherichia coli (大腸菌) 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: 3.1 Å | ||||||
データ登録者 | Harkness, R.W. / Ripstein, Z.A. / Di Trani, J.M. / Kay, L.E. | ||||||
資金援助 | カナダ, 1件
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引用 | ジャーナル: J Am Chem Soc / 年: 2023 タイトル: Flexible Client-Dependent Cages in the Assembly Landscape of the Periplasmic Protease-Chaperone DegP. 著者: Robert W Harkness / Zev A Ripstein / Justin M Di Trani / Lewis E Kay / 要旨: The periplasmic protein DegP, which is implicated in virulence factor transport leading to pathogenicity, is a bi-functional protease and chaperone that helps to maintain protein homeostasis in Gram- ...The periplasmic protein DegP, which is implicated in virulence factor transport leading to pathogenicity, is a bi-functional protease and chaperone that helps to maintain protein homeostasis in Gram-negative bacteria and is essential to bacterial survival under stress conditions. To perform these functions, DegP captures clients inside cage-like structures, which we have recently shown to form through the reorganization of high-order preformed apo oligomers, consisting of trimeric building blocks, that are structurally distinct from client-bound cages. Our previous studies suggested that these apo oligomers may allow DegP to encapsulate clients of various sizes under protein folding stresses by forming ensembles that can include extremely large cage particles, but how this occurs remains an open question. To explore the relation between cage and substrate sizes, we engineered a series of DegP clients of increasing hydrodynamic radii and analyzed their influence on DegP cage formation. We used dynamic light scattering and cryogenic electron microscopy to characterize the hydrodynamic properties and structures of the DegP cages that are adopted in response to each client. We present a series of density maps and structural models that include those for novel particles of approximately 30 and 60 monomers. Key interactions between DegP trimers and the bound clients that stabilize the cage assemblies and prime the clients for catalysis are revealed. We also provide evidence that DegP can form cages which approach subcellular organelles in terms of size. | ||||||
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 | 8f0u.cif.gz | 149.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8f0u.ent.gz | 117.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8f0u.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 | 8f0u_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8f0u_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 8f0u_validation.xml.gz | 28.4 KB | 表示 | |
CIF形式データ | 8f0u_validation.cif.gz | 39.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/f0/8f0u ftp://data.pdbj.org/pub/pdb/validation_reports/f0/8f0u | HTTPS FTP |
-関連構造データ
関連構造データ | 28781MC 8f0aC 8f1tC 8f1uC 8f21C 8f26C 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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3 |
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対称性 | 点対称性: (シェーンフリース記号: T (正4面体型対称)) |
-要素
#1: タンパク質 | 分子量: 36376.176 Da / 分子数: 1 / 断片: protease and PDZ1 domains (UNP residues 38-385) / 由来タイプ: 組換発現 由来: (組換発現) Escherichia coli (strain K12) (大腸菌) 株: K12 / 遺伝子: degP, htrA, ptd, b0161, JW0157 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0C0V0, peptidase Do |
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#2: タンパク質 | 分子量: 7970.229 Da / 分子数: 1 / 断片: PDZ2 domain (UNP residues 400-474) / 由来タイプ: 組換発現 由来: (組換発現) Escherichia coli (strain K12) (大腸菌) 株: K12 / 遺伝子: degP, htrA, ptd, b0161, JW0157 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0C0V0, peptidase Do |
#3: タンパク質・ペプチド | 分子量: 3417.168 Da / 分子数: 1 / 断片: UNP residues 404-430 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TERF1, PIN2, TRBF1, TRF, TRF1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P54274 |
-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: Structure of a 12mer DegP cage bound to the client protein hTRF1 タイプ: COMPLEX / Entity ID: all / 由来: MULTIPLE SOURCES |
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由来(天然) | 生物種: Escherichia coli (strain K12) (大腸菌) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 7 |
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-PROPANE |
-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): 2000 nm / 最小 デフォーカス(公称値): 900 nm |
撮影 | 電子線照射量: 45 e/Å2 フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) |
-解析
ソフトウェア | 名称: UCSF ChimeraX / バージョン: 1.4/v9 / 分類: モデル構築 / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / タイプ: package |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 483190 / 対称性のタイプ: POINT |