+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1gh6 | ||||||
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タイトル | RETINOBLASTOMA POCKET COMPLEXED WITH SV40 LARGE T ANTIGEN | ||||||
要素 |
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キーワード | ANTITUMOR PROTEIN / TUMOR SUPPRESSOR (がん抑制遺伝子) / ONCOPROTEIN (がん遺伝子) | ||||||
機能・相同性 | 機能・相同性情報 Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of centromere complex assembly / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / positive regulation of collagen fibril organization / negative regulation of tau-protein kinase activity / Rb-E2F complex / regulation of centromere complex assembly / regulation of lipid kinase activity / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / cell morphogenesis involved in neuron differentiation / chromatin lock complex / sister chromatid biorientation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / positive regulation of extracellular matrix organization / Aberrant regulation of mitotic exit in cancer due to RB1 defects / positive regulation of mitotic metaphase/anaphase transition / positive regulation of macrophage differentiation / tissue homeostasis / glial cell apoptotic process / protein localization to chromosome, centromeric region / negative regulation of protein serine/threonine kinase activity / bidirectional double-stranded viral DNA replication / importin-alpha family protein binding / negative regulation of hepatocyte apoptotic process / positive regulation of transcription regulatory region DNA binding / neuron maturation / digestive tract development / viral DNA genome replication / aortic valve morphogenesis / SWI/SNF complex / myoblast differentiation / negative regulation of cold-induced thermogenesis / Replication of the SARS-CoV-1 genome / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / DNA unwinding involved in DNA replication / hepatocyte apoptotic process / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / DNA replication origin binding / skeletal muscle cell differentiation / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of apoptotic signaling pathway / negative regulation of cell cycle / chromosome organization / glial cell proliferation / chondrocyte differentiation / heterochromatin formation / negative regulation of smoothened signaling pathway / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / helicase activity / phosphoprotein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / G1/S transition of mitotic cell cycle / negative regulation of protein kinase activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Oncogene Induced Senescence / negative regulation of DNA-binding transcription factor activity / negative regulation of cell growth / PML body / spindle / kinase binding / negative regulation of inflammatory response / cellular response to insulin stimulus / transcription corepressor activity / neuron projection development / Cyclin D associated events in G1 / disordered domain specific binding / negative regulation of epithelial cell proliferation / cellular response to xenobiotic stimulus / single-stranded DNA binding / Replication of the SARS-CoV-2 genome / double-stranded DNA binding / 精子形成 / symbiont-mediated perturbation of host ubiquitin-like protein modification / neuron apoptotic process / DNA-binding transcription factor binding / Ras protein signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / 細胞分化 / molecular adaptor activity / regulation of cell cycle / hydrolase activity / クロマチンリモデリング / 細胞分裂 / negative regulation of gene expression / negative regulation of DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ubiquitin protein ligase binding 類似検索 - 分子機能 | ||||||
生物種 | Simian virus 40 (ウイルス) Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 3.2 Å | ||||||
データ登録者 | Kim, H.Y. / Cho, Y. | ||||||
引用 | ジャーナル: EMBO J. / 年: 2001 タイトル: Structural basis for the inactivation of retinoblastoma tumor suppressor by SV40 large T antigen. 著者: Kim, H.Y. / Ahn, B.Y. / Cho, Y. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1gh6.cif.gz | 102 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1gh6.ent.gz | 78 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1gh6.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/gh/1gh6 ftp://data.pdbj.org/pub/pdb/validation_reports/gh/1gh6 | HTTPS FTP |
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-関連構造データ
関連構造データ | 1guxS S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 13436.985 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Simian virus 40 (ウイルス) / 属: Polyomavirusポリオーマウイルス科 / プラスミド: PET15 / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21 参照: UniProt: P03070, 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 |
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#2: タンパク質 | 分子量: 39026.504 Da / 分子数: 1 / Fragment: UNP residues 379-577 and 645-772 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: P06400 |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 3.7 Å3/Da / 溶媒含有率: 66.79 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 7.2 / 詳細: pH 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 7.5 / 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 200 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.5418 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2000年3月1日 / 詳細: MIRRORS |
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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 3.2→99 Å / Num. obs: 12666 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / 冗長度: 4.2 % / Rmerge(I) obs: 0.084 / Rsym value: 0.106 / Net I/σ(I): 15.9 |
反射 シェル | 解像度: 3.2→3.29 Å / 冗長度: 4 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.369 / % possible all: 97.2 |
反射 | *PLUS 最低解像度: 20 Å / Num. measured all: 50139 |
反射 シェル | *PLUS % possible obs: 97.2 % / Rmerge(I) obs: 0.369 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 1GUX 解像度: 3.2→19.92 Å / Rfactor Rfree error: 0.013 / 交差検証法: THROUGHOUT / σ(F): 0
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原子変位パラメータ | Biso mean: 44.2 Å2
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精密化ステップ | サイクル: LAST / 解像度: 3.2→19.92 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3.2→3.4 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 3.2 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 44.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: c_angle_deg / Dev ideal: 1.44 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | *PLUS Rfactor Rfree: 0.445 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.377 |