PDB-1ud7: SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBI...

基本情報

• 登録情報: データベース: PDB / ID: 1ud7
• タイトル: SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7
• 要素: PROTEIN (UBIQUITIN CORE MUTANT 1D7)
• キーワード: UBIQUITIN / DESIGNED CORE MUTANT

機能・相同性

分子機能:

: / : / 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 / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / cytosolic ribosome / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Iron uptake and transport / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD

ドメイン・相同性:

Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / 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

構成要素:

Ubiquitin-60S ribosomal protein L40 / Polyubiquitin-C

• 手法: 溶液NMR / RESTRAINED MOLECULAR DYNAMICS, SIULATED ANNEALING USING THE ARIA PROCEDURE OF NILGES (NILGES ET AL. (1997) J MOL BIOL 269, 408-422), EXPLICIT SWAPPING OF NON-STEREOSPECIFICALLY ASSIGNED METHYLS, METHYLENES (FOLMER ET AL., NILGES (1997) J BIOMOL NMR 9, 245-258).
• データ登録者: Johnson, E.C. / Lazar, G.A. / Desjarlais, J.R. / Handel, T.M.
• 引用: 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

登録	1999年4月7日	登録サイト: BNL / 処理サイト: RCSB
改定 1.0	1999年5月6日	Provider: repository / タイプ: Initial release
改定 1.1	2008年4月26日	Group: Version format compliance
改定 1.2	2011年7月13日	Group: Version format compliance
改定 1.3	2021年11月3日	Group: Database references / Derived calculations カテゴリ: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
改定 1.4	2023年12月27日	Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

集合体

登録構造単位

A: PROTEIN (UBIQUITIN CORE MUTANT 1D7)

概要:

• 8.6 kDa, 1 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	8,597	1
ポリマ－	8,597	1
非ポリマー	0	0
水	0	0

1

概要:

• 登録構造と同一
• 登録者が定義した集合体

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555		1

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 / 40	LOWEST ENERGY
代表モデル	モデル #1

要素

#1: タンパク質

A PROTEIN (UBIQUITIN CORE MUTANT 1D7)

詳細:

分子量: 8596.819 Da / 分子数: 1 / 変異: I3V,V5L,I13V,L15I,I23V,V26F,I67L / 由来タイプ: 組換発現 / 細胞内の位置 (発現宿主): CYTOPLASM / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): PLYSS / 参照: UniProt: P02248, UniProt: P0CG48*PLUS

実験情報

実験

• 実験: 手法: 溶液NMR

NMR実験

Conditions-ID	Experiment-ID	Solution-ID	タイプ
1	1	1	15N EDITED 3D NOESY
1	2	1	13C EDITED 3D NOESY
1	3	1	13C/13C EDITED 4D NOESY
1	4	1	3D 3JHNHA
1	5	1	3D HACAHB
1	6	1	2D 3JNCG
1	7	1	2D 3JCOCG
1	8	1	LONG RANGE 3JCC
1	9	1	3D 15N ROESY
1	10	1	3D 15N TOCSY
1	11	1	1DNH RESIDUAL DIPOLAR COUPLINGS

• NMR実験の詳細: Text: THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY ON 13C, 15N LABELED UBIQUITIN 1D7.

試料調製

• 試料状態: pH: 5.8 / 圧: 1 atm / 温度: 303.0 K
• 結晶化: 手法: other / 詳細: NMR

NMR測定

• NMRスペクトロメーター: タイプ: Bruker DMX600 / 製造業者: Bruker / モデル: DMX600 / 磁場強度: 600 MHz

解析

NMR software

名称	バージョン	開発者	分類
X-PLOR	3.851	BRUNGER	精密化
X-PLOR			構造決定

• 精密化: 手法: RESTRAINED MOLECULAR DYNAMICS, SIULATED ANNEALING USING THE ARIA PROCEDURE OF NILGES (NILGES ET AL. (1997) J MOL BIOL 269, 408-422), EXPLICIT SWAPPING OF NON-STEREOSPECIFICALLY ASSIGNED METHYLS, METHYLENES (FOLMER ET AL., NILGES (1997) J BIOMOL NMR 9, 245-258).; ソフトェア番号: 1 ; 詳細: REFINEMENT DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE
• NMRアンサンブル: コンフォーマー選択の基準: LOWEST ENERGY / 計算したコンフォーマーの数: 40 / 登録したコンフォーマーの数: 20