+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-28754 | |||||||||
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タイトル | Client-bound structure of a DegP trimer within a 12mer cage | |||||||||
マップデータ | Local refinement cryo-EM map of a DegP trimer bound to the client hTRF1. The trimer is within a 12mer cage structure. | |||||||||
試料 |
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キーワード | Protease / chaperone / hydrolase / 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 (strain K12) (大腸菌) / Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.6 Å | |||||||||
データ登録者 | Harkness RW / Ripstein ZA / Di Trani JM / Kay LE | |||||||||
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
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_28754.map.gz | 31.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-28754-v30.xml emd-28754.xml | 15.6 KB 15.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_28754_fsc.xml | 8.8 KB | 表示 | FSCデータファイル |
画像 | emd_28754.png | 40.8 KB | ||
Filedesc metadata | emd-28754.cif.gz | 5.5 KB | ||
その他 | emd_28754_half_map_1.map.gz emd_28754_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-28754 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28754 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_28754_validation.pdf.gz | 654.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_28754_full_validation.pdf.gz | 654.3 KB | 表示 | |
XML形式データ | emd_28754_validation.xml.gz | 16.3 KB | 表示 | |
CIF形式データ | emd_28754_validation.cif.gz | 21 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28754 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28754 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_28754.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Local refinement cryo-EM map of a DegP trimer bound to the client hTRF1. The trimer is within a 12mer cage structure. | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: #1
ファイル | emd_28754_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_28754_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Complex of a DegP trimer and the client protein hTRF1 from a 12me...
全体 | 名称: Complex of a DegP trimer and the client protein hTRF1 from a 12mer cage structure |
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要素 |
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-超分子 #1: Complex of a DegP trimer and the client protein hTRF1 from a 12me...
超分子 | 名称: Complex of a DegP trimer and the client protein hTRF1 from a 12mer cage structure タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Escherichia coli (strain K12) (大腸菌) |
-分子 #1: Periplasmic serine endoprotease DegP
分子 | 名称: Periplasmic serine endoprotease DegP / タイプ: protein_or_peptide / ID: 1 / コピー数: 3 / 光学異性体: LEVO / EC番号: peptidase Do |
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由来(天然) | 生物種: Escherichia coli (strain K12) (大腸菌) / 株: K12 |
分子量 | 理論値: 36.376176 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MPSLAPMLEK VMPSVVSINV EGSTTVNTPR MPRNFQQFFG DDSPFCQEGS PFQSSPFCQG GQGGNGGGQQ QKFMALGSGV IIDADKGYV VTNNHVVDNA TVIKVQLSDG RKFDAKMVGK DPRSDIALIQ IQNPKNLTAI KMADSDALRV GDYTVAIGNP F GLGETVTS ...文字列: MPSLAPMLEK VMPSVVSINV EGSTTVNTPR MPRNFQQFFG DDSPFCQEGS PFQSSPFCQG GQGGNGGGQQ QKFMALGSGV IIDADKGYV VTNNHVVDNA TVIKVQLSDG RKFDAKMVGK DPRSDIALIQ IQNPKNLTAI KMADSDALRV GDYTVAIGNP F GLGETVTS GIVSALGRSG LNAENYENFI QTDAAINRGN AGGALVNLNG ELIGINTAIL APDGGNIGIG FAIPSNMVKN LT SQMVEYG QVKRGELGIM GTELNSELAK AMKVDAQRGA FVSQVLPNSS AAKAGIKAGD VITSLNGKPI SSFAALRAQV GTM PVGSKL TLGLLRDGKQ VNVNLELQQS SQ UniProtKB: Periplasmic serine endoprotease DegP |
-分子 #2: Periplasmic serine endoprotease DegP
分子 | 名称: Periplasmic serine endoprotease DegP / タイプ: protein_or_peptide / ID: 2 / コピー数: 3 / 光学異性体: LEVO / EC番号: peptidase Do |
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由来(天然) | 生物種: Escherichia coli (strain K12) (大腸菌) / 株: K12 |
分子量 | 理論値: 7.970229 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: AEMSNKGKDQ GVVVNNVKTG TPAAQIGLKK GDVIIGANQQ AVKNIAELRK VLDSKPSVLA LNIQRGDSTI YLLMQ UniProtKB: Periplasmic serine endoprotease DegP |
-分子 #3: Telomeric repeat-binding factor 1
分子 | 名称: Telomeric repeat-binding factor 1 / タイプ: protein_or_peptide / ID: 3 / コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 3.417168 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: SKILLHYKFN NRTSVMLKDR WRTMKKL UniProtKB: Telomeric repeat-binding factor 1 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7 |
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凍結 | 凍結剤: ETHANE-PROPANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 平均電子線量: 45.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.9 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |