+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2bf8 | ||||||
---|---|---|---|---|---|---|---|
タイトル | Crystal structure of SUMO modified ubiquitin conjugating enzyme E2- 25K | ||||||
要素 |
| ||||||
キーワード | LIGASE / LIGASE-COMPLEX / E2-25K / E2 UBIQUITIN CONJUGATING ENZYME / SUMO / SUMO-TARGET STRUCTURE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS | ||||||
機能・相同性 | 機能・相同性情報 Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / Antigen processing: Ubiquitination & Proteasome degradation / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / Antigen processing: Ubiquitination & Proteasome degradation / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / septin ring / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / E2 ubiquitin-conjugating enzyme / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / negative regulation of DNA binding / ubiquitin-like protein ligase binding / ubiquitin conjugating enzyme activity / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / potassium channel regulator activity / protein K48-linked ubiquitination / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein polyubiquitination / ubiquitin-protein transferase activity / protein tag activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / protein stabilization / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | BOS TAURUS (ウシ) HOMO SAPIENS (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å | ||||||
データ登録者 | Pichler, A. / Knipscheer, P. / Oberhofer, E. / Van Dijk, W.J. / Korner, R. / Velgaard Olsen, J. / Jentsch, S. / Melchior, F. / Sixma, T.K. | ||||||
引用 | ジャーナル: Nat.Struct.Mol.Biol. / 年: 2005 タイトル: Sumo Imodification of the Ubiquitin Conjugating Enzyme E2-25K 著者: Pichler, A. / Knipscheer, P. / Oberhofer, E. / Van Dijk, W.J. / Korner, R. / Velgaard Olsen, J. / Jentsch, S. / Melchior, F. / Sixma, T.K. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 2bf8.cif.gz | 60.8 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb2bf8.ent.gz | 45 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2bf8.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
文書・要旨 | 2bf8_validation.pdf.gz | 421.2 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 2bf8_full_validation.pdf.gz | 424.2 KB | 表示 | |
XML形式データ | 2bf8_validation.xml.gz | 11.7 KB | 表示 | |
CIF形式データ | 2bf8_validation.cif.gz | 15.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/bf/2bf8 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/2bf8 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-要素
#1: タンパク質 | 分子量: 17846.412 Da / 分子数: 1 / 断片: CONSERVED CORE DOMAIN, RESIDUES 1-154 / 由来タイプ: 組換発現 詳細: COVALENT ISOPEPTIDE LINK BETWEEN E2-25K LYSINE 14 AND SUMO C-TERMINUS 由来: (組換発現) BOS TAURUS (ウシ) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P61085, ubiquitin-protein ligase |
---|---|
#2: タンパク質 | 分子量: 8970.248 Da / 分子数: 1 / 断片: RESIDUES 21-97 / 由来タイプ: 組換発現 詳細: COVALENT ISOPEPTIDE LINK BETWEEN E2-25K LYSINE 14 AND SUMO C-TERMINUS 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P63165 |
#3: 水 | ChemComp-HOH / |
配列の詳細 | COVALENT ISOPEPTIDE |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 20 |
---|
-試料調製
結晶 | マシュー密度: 2.4 Å3/Da / 溶媒含有率: 48.2 % |
---|---|
結晶化 | pH: 8.5 詳細: 100 MM TRIS PH 8.5 200 MM MAGNESIUM CHLORIDE 17% PEG 4000 10 % GLYCEROL |
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID14-4 / 波長: 0.939 |
検出器 | タイプ: ADSC ADSC Q4R / 日付: 2003年9月7日 / 詳細: TOROIDAL MIRROR |
放射 | モノクロメーター: DOUBLE CRYSTAL, SI(111), SI(311) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.939 Å / 相対比: 1 |
反射 | 解像度: 2.3→50 Å / Num. obs: 13257 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / 冗長度: 13.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.6 |
反射 シェル | 解像度: 2.3→2.42 Å / 冗長度: 13 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5 |
-解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 1FZY 解像度: 2.3→55.05 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.029 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.258 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 53.66 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→55.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
|