PDB-2den: Solution Structure of the Ubiquitin-Associated Domain of Human BM...

基本情報

• 登録情報: データベース: PDB / ID: 2den
• タイトル: Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin

要素

• Immunoglobulin G-binding protein G,Ubiquitin-like protein 7
• Polyubiquitin-B

• キーワード: PROTEIN BINDING / A:alpha-alpha-alpha / B:beta-beta-helix-helix-beta-beta-helix-beta

機能・相同性

分子機能:

IgG binding / polyubiquitin modification-dependent protein binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / antiviral innate immune response / 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 / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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 / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / 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 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Stabilization of p53 / Hh mutants are degraded by ERAD / Negative regulation of FGFR4 signaling / Activation of NF-kappaB in B cells / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / EGFR downregulation / Degradation of GLI1 by the proteasome / Termination of translesion DNA synthesis / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis

ドメイン・相同性:

: / : / : / IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-associated (UBA) domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / YSIRK Gram-positive signal peptide / UBA-like superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Helicase, Ruva Protein; domain 3 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta

構成要素:

Ubiquitin B / Immunoglobulin G-binding protein G / Polyubiquitin-C / Ubiquitin-like protein 7

• 生物種: Streptococcus sp. group G (バクテリア); Homo sapiens (ヒト)
• 手法: 溶液NMR / molecular dynamics
• データ登録者: Hu, H.Y. / Lin, D.H. / Chang, Y.G.
• 引用: ジャーナル: Protein Sci. / 年: 2006; タイトル: Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin; 著者: Chang, Y.G. / Song, A.X. / Gao, Y.G. / Shi, Y.H. / Lin, X.J. / Cao, X.T. / Lin, D.H. / Hu, H.Y.

履歴

登録	2006年2月14日	登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.0	2006年6月13日	Provider: repository / タイプ: Initial release
改定 1.1	2008年4月30日	Group: Version format compliance
改定 1.2	2011年7月13日	Group: Version format compliance
改定 1.3	2020年1月15日	Group: Database references / Derived calculations / Source and taxonomy / Structure summary カテゴリ: entity / entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.details / _entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
改定 1.4	2024年5月1日	Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

集合体

登録構造単位

A: Immunoglobulin G-binding protein G,Ubiquitin-like protein 7

B: Polyubiquitin-B

概要:

• 20.5 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)	20,485	2
ポリマ－	20,485	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		1

計算値:

Buried area	1570 Å2
ΔGint	-6 kcal/mol
Surface area	6530 Å2

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	structures with the lowest energy
代表モデル	モデル #1	lowest energy

要素

#1: 抗体

A Immunoglobulin G-binding protein G,Ubiquitin-like protein 7 / IgG-binding protein G / Bone marrow stromal cell ubiquitin-like protein / BMSC-UbP / Ubiquitin-like protein SB132

詳細:

分子量: 11908.023 Da / 分子数: 1 / 断片: UBA domain,UBA domain / 変異: I12A / 由来タイプ: 組換発現
詳細: HGB1-UBA is a chimeric protein. The N-terminal HisTag is for ease of purification. The GB1 domain is used for solubility enhancement. The GB1 domain sequence refers to the protein with accession code P06654.,HGB1-UBA is a chimeric protein. The N-terminal HisTag is for ease of purification. The GB1 domain is used for solubility enhancement. The GB1 domain sequence refers to the protein with accession code P06654.
由来: (組換発現) Streptococcus sp. group G (バクテリア), (組換発現) Homo sapiens (ヒト)
属: Streptococcus, Homo / 生物種: , / 遺伝子: spg, UBL7, BMSCUBP, SB132 / プラスミド: pHGB / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) CodonPlus / 参照: UniProt: P06654, UniProt: Q96S82

#2: タンパク質

B Polyubiquitin-B

詳細:

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: UBB / プラスミド: pET-3a / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: J3QS39, 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	titration of sample 1 with sample 2
1	2	2	titration of sample 2 with sample 1

• NMR実験の詳細: Text: This complex model is constructed by using the HADDOCK program which employs the Ambiguous Interaction Restraints (AIR) that are obtained from the reciprocal NMR titration of the two samples.

試料調製

詳細

Solution-ID	内容	溶媒系
1	1mM HGB1-UBA	20mM phosphate, 100mM NaCl, pH6.5
2	1mM Ubiquitin	20mM phosphate, 100mM NaCl, pH6.5

• 試料状態: pH: 6.5 / 圧: ambient / 温度: 298 K

NMR測定

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

解析

NMR software

名称	バージョン	開発者	分類
HADDOCK	1.3	Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin	精密化
HADDOCK	1.3	Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin	構造決定

• 精密化: 手法: molecular dynamics / ソフトェア番号: 1 ; 詳細: Based on NMR titration data, the complex structrue is constructed using the HADDOCK program.
• 代表構造: 選択基準: lowest energy
• 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: 200 / 登録したコンフォーマーの数: 10