+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1fmo | ||||||
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タイトル | CRYSTAL STRUCTURE OF A POLYHISTIDINE-TAGGED RECOMBINANT CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE COMPLEXED WITH THE PEPTIDE INHIBITOR PKI(5-24) AND ADENOSINE | ||||||
要素 |
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キーワード | COMPLEX (PHOSPHOTRANSFERASE/INHIBITOR) / COMPLEX (PHOSPHOTRANSFERASE-INHIBITOR) / PHOSPHORYLATION / POLYHISTIDINE-TAG / PROTEIN KINASE / COMPLEX (PHOSPHOTRANSFERASE-INHIBITOR) complex | ||||||
機能・相同性 | 機能・相同性情報 spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / negative regulation of cAMP-dependent protein kinase activity / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / Mitochondrial protein degradation / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / molecular function inhibitor activity / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / regulation of G2/M transition of mitotic cell cycle / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / sperm midpiece / negative regulation of TORC1 signaling / regulation of synaptic transmission, glutamatergic / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / small GTPase binding / mRNA processing / presynapse / peptidyl-serine phosphorylation / manganese ion binding / cellular response to heat / postsynapse / dendritic spine / molecular adaptor activity / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / positive regulation of cell population proliferation / ubiquitin protein ligase binding / glutamatergic synapse / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) | ||||||
手法 | X線回折 / 同系置換 / 解像度: 2.2 Å | ||||||
データ登録者 | Narayana, N. / Cox, S. / Shaltiel, S. / Taylor, S.S. / Xuong, N.-H. | ||||||
引用 | ジャーナル: Biochemistry / 年: 1997 タイトル: Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine. 著者: Narayana, N. / Cox, S. / Shaltiel, S. / Taylor, S.S. / Xuong, N. #1: ジャーナル: Structure / 年: 1997 タイトル: A Binary Complex of the Catalytic Subunit of Camp-Dependent Protein Kinase and Adenosine Further Defines Conformational Flexibility 著者: Narayana, N. / Cox, S. / Xuong, N.H. / Ten Eyck, L.F. / Taylor, S.S. #2: ジャーナル: Biochemistry / 年: 1993 タイトル: Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with Mgatp and Peptide Inhibitor 著者: Zheng, J. / Knighton, D.R. / Ten Eyck, L.F. / Karlsson, R. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. #3: ジャーナル: Protein Eng. / 年: 1993 タイトル: Expression of the Catalytic Subunit of Camp-Dependent Protein Kinase in Escherichia Coli: Multiple Isozymes Reflect Different Phosphorylation States 著者: Herberg, F.W. / Bell, S.M. / Taylor, S.S. #4: ジャーナル: Science / 年: 1991 タイトル: Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase 著者: Knighton, D.R. / Zheng, J.H. / Ten Eyck, L.F. / Ashford, V.A. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. #5: ジャーナル: Science / 年: 1991 タイトル: Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase 著者: Knighton, D.R. / Zheng, J.H. / Ten Eyck, L.F. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. | ||||||
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 | 1fmo.cif.gz | 85.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1fmo.ent.gz | 67 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1fmo.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 | 1fmo_validation.pdf.gz | 458.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1fmo_full_validation.pdf.gz | 481 KB | 表示 | |
XML形式データ | 1fmo_validation.xml.gz | 11.9 KB | 表示 | |
CIF形式データ | 1fmo_validation.cif.gz | 17.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fm/1fmo ftp://data.pdbj.org/pub/pdb/validation_reports/fm/1fmo | HTTPS FTP |
-関連構造データ
関連構造データ | 1apmS 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 40657.316 Da / 分子数: 1 / 断片: CATALYTIC SUBUNIT / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 器官: SKELETAL / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P05132, EC: 2.7.1.37 |
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#2: タンパク質・ペプチド | 分子量: 2226.411 Da / 分子数: 1 / 断片: RESIDUES 5 - 24 / 由来タイプ: 組換発現 / 参照: UniProt: P61926 |
#3: 化合物 | ChemComp-ADN / |
#4: 水 | ChemComp-HOH / |
-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: 2.7 Å3/Da / 溶媒含有率: 54 % | ||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 詳細: ORTHORHOMBIC CRYSTALS OF THE TERNARY COMPLEX, COMPRISED OF MOUSE HIS6-RC SUBUNIT, PKI (5-24) AND ADENOSINE, WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD USING 2-METHYL-2,4- ...詳細: ORTHORHOMBIC CRYSTALS OF THE TERNARY COMPLEX, COMPRISED OF MOUSE HIS6-RC SUBUNIT, PKI (5-24) AND ADENOSINE, WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD USING 2-METHYL-2,4-PENTANEDIOL (MPD) AS THE PRECIPITATING AGENT. THE MOTHER-LIQUOR CONTAINED PROTEIN AT A CONCENTRATION OF 0.25 MM IN 100 MM BICINE BUFFER AT PH 8.0, 0.75 MM PKI(5-24), 4 MM ADENOSINE AND 4% MPD. THE RESERVOIR SOLUTION WAS MADE UP OF 20% MPD IN 100 MM BICINE BUFFER (PH 8.0). X-RAY DIFFRACTION QUALITY CRYSTALS (0.2 X 0.15 X 0.8 MM3) WERE GROWN AT 4 C IN APPROXIMATELY 4 - 6 WEEKS., vapor diffusion - hanging drop, temperature 277K | ||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / 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: 277 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RUH2R / 波長: 1.5418 |
検出器 | タイプ: XUONG-HAMLIN MULTIWIRE / 検出器: AREA DETECTOR / 日付: 1994年2月7日 |
放射 | モノクロメーター: GRAPHITE(002) / 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: 2.2→20 Å / Num. obs: 21679 / % possible obs: 92 % / Observed criterion σ(I): 0 / 冗長度: 2.4 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.064 / Net I/σ(I): 7.3 |
反射 シェル | 解像度: 2.2→2.3 Å / 冗長度: 1.4 % / Mean I/σ(I) obs: 1 / Rsym value: 0.25 / % possible all: 84 |
反射 | *PLUS Rmerge(I) obs: 0.064 |
反射 シェル | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.25 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 同系置換 開始モデル: PDB ENTRY 1APM 解像度: 2.2→10 Å / σ(F): 1 /
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溶媒の処理 | Bsol: 167.1 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.2→10 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: TNT / バージョン: 5E / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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