+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4a0c | ||||||
---|---|---|---|---|---|---|---|
タイトル | Structure of the CAND1-CUL4B-RBX1 complex | ||||||
要素 |
| ||||||
キーワード | CELL CYCLE / TRANSCRIPTION / LIGASE / UBIQUITIN / DNA DAMAGE REPAIR | ||||||
機能・相同性 | 機能・相同性情報 Prolactin receptor signaling / SCF complex assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER ...Prolactin receptor signaling / SCF complex assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / Degradation of beta-catenin by the destruction complex / eukaryotic initiation factor 4E binding / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / anaphase-promoting complex / GLI3 is processed to GLI3R by the proteasome / negative regulation of catalytic activity / cullin-RING-type E3 NEDD8 transferase / Neddylation / cullin-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / VCB complex / astrocyte differentiation / positive regulation of protein autoubiquitination / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / protein monoubiquitination / cullin family protein binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasomal protein catabolic process / positive regulation of G1/S transition of mitotic cell cycle / protein K48-linked ubiquitination / ubiquitin ligase complex / positive regulation of TORC1 signaling / T cell activation / TBP-class protein binding / Recognition of DNA damage by PCNA-containing replication complex / cellular response to amino acid stimulus / Iron uptake and transport / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / protein catabolic process / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / G1/S transition of mitotic cell cycle / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / neuron projection development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome biogenesis / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / ficolin-1-rich granule lumen / cell differentiation / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / protein-containing complex binding / Golgi apparatus / extracellular exosome / zinc ion binding / extracellular region 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) MUS MUSCULUS (ハツカネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.8 Å | ||||||
データ登録者 | Scrima, A. / Fischer, E.S. / Faty, M. / Gut, H. / Thoma, N.H. | ||||||
引用 | ジャーナル: Cell(Cambridge,Mass.) / 年: 2011 タイトル: The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation 著者: Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H. | ||||||
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 | 4a0c.cif.gz | 755.4 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb4a0c.ent.gz | 604 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4a0c.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/a0/4a0c ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a0c | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
単位格子 |
|
-要素
#1: タンパク質 | 分子量: 139226.281 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PFASTBAC DERIVED / 細胞株 (発現宿主): High Five / 発現宿主: TRICHOPLUSIA NI (イラクサキンウワバ) / 参照: UniProt: Q86VP6 #2: タンパク質 | 分子量: 86961.336 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PFASTBAC DERIVED / 細胞株 (発現宿主): High Five / 発現宿主: TRICHOPLUSIA NI (イラクサキンウワバ) / 参照: UniProt: Q13620 #3: タンパク質 | 分子量: 11330.942 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / プラスミド: PFASTBAC DERIVED / 細胞株 (発現宿主): High Five / 発現宿主: TRICHOPLUSIA NI (イラクサキンウワバ) 参照: UniProt: P62878, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ(ペプチド合成) #4: 化合物 | ChemComp-ZN / 配列の詳細 | CHAINS A AND B CONTAINS NATURAL VARIANT A952V | |
---|
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
---|
-試料調製
結晶 | マシュー密度: 3.52 Å3/Da / 溶媒含有率: 65.08 % 解説: CAND1 USED AS MODEL FROM 1U6G, CUL4B MODEL GENERATED USING MODELLER BASED ON CUL4A FROM 2HYE |
---|---|
結晶化 | pH: 6.3 / 詳細: 100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000. |
-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: SLS / ビームライン: X10SA / 波長: 1 |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2010年7月30日 |
放射 | 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: 1 Å / 相対比: 1 |
反射 | 解像度: 3.8→50 Å / Num. obs: 59850 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / 冗長度: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
反射 シェル | 解像度: 3.8→3.9 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8 |
-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 ENTRIES 1U6G, 2HYE 解像度: 3.8→47.76 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.882 / SU B: 56.264 / SU ML: 0.797 / 交差検証法: THROUGHOUT / ESU R Free: 0.906 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.4 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 128.578 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3.8→47.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
|