PDB-2bgf: NMR structure of Lys48-linked di-ubiquitin using chemical shift p...

基本情報

• 登録情報: データベース: PDB / ID: 2bgf
• タイトル: NMR structure of Lys48-linked di-ubiquitin using chemical shift perturbation data together with RDCs and 15N-relaxation data
• 要素: DI-UBIQUITIN
• キーワード: UBIQUITIN / PROTEASOME / DEGRADATION / POLYUBIQUITIN

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 / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / 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 / 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 / cytosolic ribosome / 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 / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / 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 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Degradation of DVL / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53

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:

Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40

• 生物種: HOMO SAPIENS (ヒト)
• 手法: 溶液NMR / HADDOCK
• データ登録者: Van Dijk, A.D.J. / Fushman, D. / Bonvin, A.M.J.J.

引用

ジャーナル: Proteins: Struct., Funct., Bioinf. / 年: 2005
タイトル: Various Strategies of Using Residual Dipolar Couplings in NMR-Driven Protein Docking: Application to Lys48-Linked Di-Ubiquitin and Validation Against 15N-Relaxation Data
著者: Van Dijk, A.D.J. / Fushman, D. / Bonvin, A.M.J.J.

#1: ジャーナル: J.Mol.Biol. / 年: 2002
タイトル: Structural Properties of Polyubiquitin Chains in Solution
著者: Varadan, R. / Walker, O. / Pickart, C. / Fushman, D.

履歴

登録	2004年12月22日	登録サイト: PDBE / 処理サイト: PDBE
改定 1.0	2005年8月31日	Provider: repository / タイプ: Initial release
改定 1.1	2011年5月8日	Group: Version format compliance
改定 1.2	2011年7月13日	Group: Version format compliance
改定 1.3	2024年5月15日	Group: Data collection / Database references / Other カテゴリ: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

集合体

登録構造単位

A: DI-UBIQUITIN

B: DI-UBIQUITIN

概要:

• 17.2 kDa, 2 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)	17,154	2
ポリマ－	17,154	2
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	x,y,z	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)	10 / 200	LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER
代表モデル	モデル #1

要素

#1: タンパク質

A B DI-UBIQUITIN / UBIQUITIN

詳細:

分子量: 8576.831 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: ISOPEPTIDE BOND BETWEEN GLY76A AND LYS48B / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P62988, UniProt: P0CG48*PLUS

• 構成要素の詳細: FUNCTIONS INCLUDE ATP-DEPENDENT SELECTIVE DEGRADATION OF CELLULAR PROTEINS, MAINTENANCE OF CHROMATIN STRUCTURE, REGULATION OF GENE EXPRESSION, STRESS RESPONSE, AND RIBOSOME BIOGENESIS

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	HSQC
1	2	1	TOCSY

• NMR実験の詳細: Text: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING CHEMICAL SHIFT PERTURBATION DATA AS AMBIGUOUS INTERACTION RESTRAINTS AND RESIDUAL DIPOLAR COUPLINGS BOTH AS DIRECT RESTRAINTS (SANI) AND INTERVECTOR PROJECTION ANGLE RESTRAINTS (VEAN). STRUCTURAL CHARACTERISTICS OF ENSEMBLE OF 10 BEST: AVERAGE (STANDARD DEVIATION) INTERMOLECULAR ENERGIES RAMACHANDRAN ANALYSIS:

試料調製

• 詳細: 内容: 90% WATER/10% D20
• 試料状態: イオン強度: 20 mM / pH: 6.8 / 圧: 1.0 atm / 温度: 298.0 K

NMR測定

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

解析

NMR software

名称	開発者	分類
HADDOCK	DOMINGUEZ, BOELENS,BONVIN	精密化
HADDOCK		構造決定

• 精密化: 手法: HADDOCK / ソフトェア番号: 1 ; 詳細: REFINEMENT IS DONE IN EXPLICIT SOLVENT. REFINEMENT AND STRUCTURE CALCULATION DETAILS CAN BE FOUND IN DOMINGUEZ ET AL, JACS 2003, 125, 173
• NMRアンサンブル: コンフォーマー選択の基準: LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER; 計算したコンフォーマーの数: 200 / 登録したコンフォーマーの数: 10