+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1c3t | ||||||
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タイトル | ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY | ||||||
要素 | PROTEIN (1D8 UBIQUITIN) | ||||||
キーワード | DE NOVO PROTEIN (De novo) / PROTEIN DESIGN (タンパク質設計) / HYDROPHOBIC CORE (疎水効果) / PACKING / ROTAMERS / ROC / UBIQUITIN (ユビキチン) | ||||||
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 / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / 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 / cytosolic ribosome / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / 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 / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 溶液NMR / RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING USING THE ARIA PROCEDURE OF NILGES (NILGES ET AL., J MOL BIOL, 1997, 269: 408- 422), EXPLICIT SWAPPING OF NON- STEREOSPECIFICALLY ASSIGNED METHYLS, METHYLENES (FOLMER ET AL. J BIOMOL NMR, 1997, 9: 245-258). | ||||||
データ登録者 | Lazar, G.A. / Johnson, E.C. / Desjarlais, J.R. / Handel, T.M. | ||||||
引用 | ジャーナル: Protein Sci. / 年: 1999 タイトル: Rotamer strain as a determinant of protein structural specificity. 著者: Lazar, G.A. / Johnson, E.C. / Desjarlais, J.R. / Handel, T.M. #1: ジャーナル: Protein Sci. / 年: 1997 タイトル: De Novo Design of the Hydrophobic Core of Ubiquitin 著者: Lazar, G.A. / Desjarlais, J.R. / Handel, T.M. #2: ジャーナル: Structure Fold.Des. / 年: 1999 タイトル: Solution Structure and Dynamics of a Designed Hydrophobic Core Variant of Ubiquitin 著者: Johnson, E.C. / Lazar, G.A. / Desjarlais, J.R. / Handel, T.M. | ||||||
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 | 1c3t.cif.gz | 479.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1c3t.ent.gz | 399.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1c3t.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/c3/1c3t ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3t | HTTPS FTP |
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-関連構造データ
-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 / 変異: I3L,I13L,L15V,V17L,I23V,V26L,I61L,L67I / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PAED4 / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P62988, UniProt: P0CG48*PLUS |
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-実験情報
-実験
実験 | 手法: 溶液NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR実験 |
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NMR実験の詳細 | Text: THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY. |
-試料調製
詳細 | 内容: 2 MM 13C/15N 1D8 UBIQUITIN, 25 MM SODIUM PHOSPHATE, 25 MM SODIUM ACETATE (D3), 0.02% SODIUM AZIDE, PH 5.8 |
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試料状態 | イオン強度: 50 mM / pH: 5.80 / 圧: 1 atm / 温度: 303.00 K |
結晶化 | *PLUS 手法: その他 / 詳細: NMR |
-NMR測定
NMRスペクトロメーター | タイプ: Bruker DMX / 製造業者: Bruker / モデル: DMX / 磁場強度: 600 MHz |
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-解析
精密化 | 手法: RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING USING THE ARIA PROCEDURE OF NILGES (NILGES ET AL., J MOL BIOL, 1997, 269: 408- 422), EXPLICIT SWAPPING OF NON- STEREOSPECIFICALLY ASSIGNED ...手法: RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING USING THE ARIA PROCEDURE OF NILGES (NILGES ET AL., J MOL BIOL, 1997, 269: 408- 422), EXPLICIT SWAPPING OF NON- STEREOSPECIFICALLY ASSIGNED METHYLS, METHYLENES (FOLMER ET AL. J BIOMOL NMR, 1997, 9: 245-258). ソフトェア番号: 1 詳細: THE STRUCTURES WERE CALCULATED USING 3212 NONREDUNDANT NOE RESTRAINTS, 84 DIHEDRAL RESTRAINTS, AND 68 H-BOND RESTRAINTS. |
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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: 30 / 登録したコンフォーマーの数: 20 |