[日本語] English
万見
- PDB-6ud0: Solution-state NMR structural ensemble of human Tsg101 UEV in com... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 6ud0
タイトルSolution-state NMR structural ensemble of human Tsg101 UEV in complex with K63-linked diubiquitin
要素
  • (Ubiquitin) x 2
  • Tumor susceptibility gene 101 protein
キーワードCELL CYCLE / ESCRT-I / viral budding / ubiquitin E2 variant
機能・相同性
機能・相同性情報


positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / positive regulation of exosomal secretion / membrane fission / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / virion binding / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / endosome to lysosome transport / female gonad development / seminiferous tubule development / viral budding via host ESCRT complex / negative regulation of epidermal growth factor receptor signaling pathway / male meiosis I / viral release from host cell / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / autophagosome maturation / energy homeostasis / keratinocyte differentiation / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / multivesicular body / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / HCMV Late Events / ubiquitin binding / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / regulation of mitochondrial membrane potential
類似検索 - 分子機能
Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. / ESCRT assembly domain / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like ...Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / : / UEV domain / UEV domain profile. / ESCRT assembly domain / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
類似検索 - ドメイン・相同性
Polyubiquitin-B / Tumor susceptibility gene 101 protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法溶液NMR / simulated annealing
データ登録者Strickland, M. / Watanabe, S. / Bonn, S.M. / Camara, C.M. / Fushman, D. / Carter, C.A. / Tjandra, N.
引用ジャーナル: Structure / 年: 2021
タイトル: Tsg101/ESCRT-I Recruitment Regulated by the Dual Binding Modes of K63-Linked Diubiquitin
著者: Strickland, M. / Watanabe, S. / Bonn, S.M. / Camara, C.M. / Fushman, D. / Carter, C.A. / Tjandra, N.
履歴
登録2019年9月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年3月17日Provider: repository / タイプ: Initial release
改定 1.12021年9月22日Group: Database references / カテゴリ: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023年6月14日Group: Other / カテゴリ: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
改定 1.32024年10月16日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
A: Ubiquitin
B: Ubiquitin
C: Tumor susceptibility gene 101 protein


分子量 (理論値)分子数
合計 (水以外)33,9303
ポリマ－33,9303
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: NMR spectroscopy was used to determine the quaternary structure.
タイプ名称対称操作数
identity operation1_5551
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)20 / 100structures with the lowest energy
代表モデルモデル #1target function

-
要素

#1: タンパク質 Ubiquitin


分子量: 8604.845 Da / 分子数: 1 / 変異: K63R / 由来タイプ: 組換発現
詳細: Distal domain of K63-linked diubiquitin. The K63R mutation is made to prevent formation of polyubiquitin during enzymatic linkage to the proximal domain. Joined to the proximal domain of ...詳細: Distal domain of K63-linked diubiquitin. The K63R mutation is made to prevent formation of polyubiquitin during enzymatic linkage to the proximal domain. Joined to the proximal domain of diubiquitin at residue G76 using an isopeptide bond.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P0CG47
#2: タンパク質 Ubiquitin


分子量: 8691.918 Da / 分子数: 1 / 変異: +D77 / 由来タイプ: 組換発現
詳細: Proximal domain of K63-linked diubiquitin. The additional aspartic acid on the C-terminus (+D77) is made to prevent formation of polyubiquitin during enzymatic linkage to the distal domain. ...詳細: Proximal domain of K63-linked diubiquitin. The additional aspartic acid on the C-terminus (+D77) is made to prevent formation of polyubiquitin during enzymatic linkage to the distal domain. Joined to the distal domain of diubiquitin at residue K63 using an isopeptide bond.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBB / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P0CG47
#3: タンパク質 Tumor susceptibility gene 101 protein / ESCRT-I complex subunit TSG101


分子量: 16633.352 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: TSG101 / プラスミド: pET-28B / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Rosetta2 / 参照: UniProt: Q99816
Has protein modificationY

-
実験情報

-
実験

実験手法: 溶液NMR
NMR実験
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDタイプ
111isotropic22D 1H-15N HSQC
188isotropic22D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
199isotropic12D 1H-15N HSQC
133isotropic12D 1H-15N HSQC
11010isotropic12D 1H-15N HSQC
144isotropic12D 1H-15N HSQC
155anisotropic12D 1H-15N HSQC
166isotropic12D 1H-15N HSQC
177anisotropic12D 1H-15N HSQC

-
試料調製

詳細
タイプSolution-ID内容詳細Label溶媒系
solution1200 uM [U-98% 15N] Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OSample used for measuring chemical shift perturbations of Tsg101 UEV domain (bound form)15NTsg_CSPs_bound93% H2O/7% D2O
solution8200 uM [U-98% 15N] Tsg101 UEV domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OSample used for measuring chemical shift perturbations of Tsg101 UEV domain (free form)15NTsg_CSPs_free93% H2O/7% D2O
solution2200 uM Tsg101 UEV domain, 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OSample used for measuring chemical shift perturbations of 15N-distal domain of diubiquitin (bound form)15NDistal_CSPs_bound93% H2O/7% D2O
solution9200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OSample used for measuring chemical shift perturbations of 15N-distal domain of diubiquitin (free form)15NDistal_CSPs_free93% H2O/7% D2O
solution3200 uM Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OSample used for measuring chemical shift perturbations of 15N-proximal domain of diubiquitin (bound form)15NProx_CSPs_bound93% H2O/7% D2O
solution10200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OSample used for measuring chemical shift perturbations of 15N-proximal domain of diubiquitin (free form)15N_Prox_CSPs_free93% H2O/7% D2O
solution4125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OThe distal domain of diubiquitin was mutated (T14C) to incorporate a covalently bound Lu-M8-DOTA-SPy tag for the measurement of pseudocontact shifts in Tsg101 UEV domain (reference).15NTsg_PCS_Dist_Lu93% H2O/7% D2O
solution5125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OThe distal domain of diubiquitin was mutated (T14C) to incorporate a covalently bound Tm-M8-DOTA-SPy tag for the measurement of pseudocontact shifts in Tsg101 UEV domain (paramagnetic).15NTsg_PCS_Dist_Tm93% H2O/7% D2O
solution6125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OThe proximal domain of diubiquitin was mutated (T14C) to incorporate a covalently bound Lu-M8-DOTA-SPy tag for the measurement of pseudocontact shifts in Tsg101 UEV domain (reference).15NTsg_PCS_Prox_Lu93% H2O/7% D2O
solution7125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2OThe proximal domain of diubiquitin was mutated (T14C) to incorporate a covalently bound Tm-M8-DOTA-SPy tag for the measurement of pseudocontact shifts in Tsg101 UEV domain (paramagnetic).15NTsg_PCS_Prox_Tm93% H2O/7% D2O
試料
濃度 (mg/ml)構成要素Isotopic labelingSolution-ID
200 uMTsg101 UEV domain[U-98% 15N]1
200 uMK63-linked diubiquitin, distal domainnatural abundance1
200 uMK63-linked diubiquitin, proximal domainnatural abundance1
20 mMpotassium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
200 uMTsg101 UEV domain[U-98% 15N]8
20 mMpotassium phosphatenatural abundance8
50 mMsodium chloridenatural abundance8
200 uMTsg101 UEV domainnatural abundance2
200 uMK63-linked diubiquitin, distal domain[U-98% 15N]2
200 uMK63-linked diubiquitin, proximal domainnatural abundance2
20 mMpotassium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
200 uMK63-linked diubiquitin, distal domain[U-98% 15N]9
200 uMK63-linked diubiquitin, proximal domainnatural abundance9
20 mMpotassium phosphatenatural abundance9
50 mMsodium chloridenatural abundance9
200 uMTsg101 UEV domainnatural abundance3
200 uMK63-linked diubiquitin, distal domainnatural abundance3
200 uMK63-linked diubiquitin, proximal domain[U-98% 15N]3
20 mMpotassium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
200 uMK63-linked diubiquitin, distal domainnatural abundance10
200 uMK63-linked diubiquitin, proximal domain[U-98% 15N]10
20 mMpotassium phosphatenatural abundance10
50 mMsodium chloridenatural abundance10
125 uMTsg101 UEV domain[U-98% 15N]4
125 uMK63-linked diubiquitin, distal domainnatural abundance4
125 uMK63-linked diubiquitin, proximal domainnatural abundance4
20 mMpotassium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
125 uMTsg101 UEV domain[U-98% 15N]5
125 uMK63-linked diubiquitin, distal domainnatural abundance5
125 uMK63-linked diubiquitin, proximal domainnatural abundance5
20 mMpotassium phosphatenatural abundance5
50 mMsodium chloridenatural abundance5
125 uMTsg101 UEV domain[U-98% 15N]6
125 uMK63-linked diubiquitin, distal domainnatural abundance6
125 uMK63-linked diubiquitin, proximal domainnatural abundance6
20 mMpotassium phosphatenatural abundance6
50 mMsodium chloridenatural abundance6
125 uMTsg101 UEV domain[U-98% 15N]7
125 uMK63-linked diubiquitin, distal domainnatural abundance7
125 uMK63-linked diubiquitin, proximal domainnatural abundance7
20 mMpotassium phosphatenatural abundance7
50 mMsodium chloridenatural abundance7
試料状態イオン強度: 0.1 M / Label: Conditions_1 / pH: 5.8 / 圧: 1 atm / 温度: 300 K

-
NMR測定

NMRスペクトロメーター
タイプ製造業者モデル磁場強度 (MHz)Spectrometer-ID詳細
Bruker AVANCEBrukerAVANCE6001Cryoprobe
Bruker AVANCEBrukerAVANCE8002Cryoprobe

-
解析

NMR software
名称バージョン開発者分類
NMRPipe9.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax解析
TopSpin3Bruker Biospincollection
CcpNmr Analysis2.4.2CCPNpeak picking
CcpNmr Analysis2.4.2CCPNchemical shift assignment
X-PLOR NIH2.51Schwieters, Kuszewski, Tjandra and Clore精密化
X-PLOR NIH2.51Schwieters, Kuszewski, Tjandra and Clorestructure calculation
精密化手法: simulated annealing / ソフトェア番号: 7
詳細: Docking was carried out between the two proteins using rigid body simulated annealing with a flexible linker between diubiquitin domains. Initial structures were 3H7P and 2MJB for ubiquitin, ...詳細: Docking was carried out between the two proteins using rigid body simulated annealing with a flexible linker between diubiquitin domains. Initial structures were 3H7P and 2MJB for ubiquitin, and 1S1Q for Tsg101 UEV. Distal domain and Tsg101 backbone were fixed to 1S1Q position. Following initial docking, the lowest energy structure in each of the two clusters was used as input for refinement, with an ensemble number of 2.
代表構造選択基準: target function
NMRアンサンブルコンフォーマー選択の基準: structures with the lowest energy
計算したコンフォーマーの数: 100 / 登録したコンフォーマーの数: 20

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る