+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2kn5 | ||||||
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タイトル | A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family | ||||||
要素 | Ubiquitinユビキチン | ||||||
キーワード | GENE REGULATION (遺伝子発現の調節) / Backrub / Residual Dipolar Coupling / Backbone flexibility / Protein dynamics / Cytoplasm (細胞質) / Isopeptide bond / Nucleus (Nucleus) / Phosphoprotein / Ubl conjugation | ||||||
機能・相同性 | 機能・相同性情報 : / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation ...: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / 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 / cytosolic ribosome / グリコーゲン合成 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 溶液NMR / Monte Carlo optimization of ensemble members | ||||||
データ登録者 | Friedland, G.D. | ||||||
引用 | ジャーナル: PLOS COMPUT.BIOL. / 年: 2009 タイトル: A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. 著者: Friedland, G.D. / Lakomek, N.A. / Griesinger, C. / Meiler, J. / Kortemme, T. | ||||||
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 | 2kn5.cif.gz | 1.2 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2kn5.ent.gz | 1 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2kn5.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/kn/2kn5 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/2kn5 | HTTPS FTP |
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-関連構造データ
関連構造データ | |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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NMR アンサンブル |
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-要素
#1: タンパク質 | 分子量: 8576.831 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: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62988, UniProt: P0CG48*PLUS |
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-実験情報
-実験
実験 | 手法: 溶液NMR 詳細: This ensemble provides a model of the structural variation present in the structured regions of ubiquitin from residual dipolar coupling measurements in 23 alignment media. | ||||||||||||
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NMR実験 |
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-試料調製
詳細 |
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試料 |
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試料状態 | イオン強度: 0.05 / pH: 6.5 / 圧: ambient / 温度: 308 K |
-NMR測定
NMRスペクトロメーター |
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-解析
NMR software |
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精密化 | 手法: Monte Carlo optimization of ensemble members / ソフトェア番号: 1 詳細: A 10,000-MEMBER SET OF STRUCTURES WAS GENERATED USING ROSETTA AND BACKRUB CONFORMATIONAL SAMPLING. THE 50-MEMBER ENSEMBLE PRESENTED HERE WAS OPTIMIZED BY SELECTING STRUCTURES FROM THIS SET ...詳細: A 10,000-MEMBER SET OF STRUCTURES WAS GENERATED USING ROSETTA AND BACKRUB CONFORMATIONAL SAMPLING. THE 50-MEMBER ENSEMBLE PRESENTED HERE WAS OPTIMIZED BY SELECTING STRUCTURES FROM THIS SET THAT MAXIMIZE AGREEMENT WITH THE RESIDUAL DIPOLAR COUPLINGS. SEVERAL OF THE STRUCTURES IN ENSEMBLE ARE IDENTICAL AS CHOSEN BY THE OPTIMIZATION ALGORITHM. | |||||||||
NMRアンサンブル | コンフォーマー選択の基準: all calculated structures submitted 計算したコンフォーマーの数: 50 / 登録したコンフォーマーの数: 50 |