+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1gy3 | |||||||||
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タイトル | pCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate | |||||||||
要素 |
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キーワード | TRANSFERASE/TRANSFERASE SUBSTRATE / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX / CELL CYCLE REGULATORY PROTEIN KINASE / THR160-PHOSPHO-CYCLIN DEPENDENT PROTEIN KINASE 2 IN ASSOCIATION WITH CYCLIN A / TRANSFERASE- TRANSFERASE SUBSTRATE COMPLEX | |||||||||
機能・相同性 | 機能・相同性情報 Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2期 / cyclin-dependent protein kinase activity / Y染色体 / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X染色体 / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / regulation of DNA replication / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / カハール体 / サイクリン依存性キナーゼ / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / male germ cell nucleus / response to organic substance / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / 遺伝的組換え / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / 細胞老化 / Regulation of TP53 Degradation / 核膜 / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / 遺伝子発現の調節 / peptidyl-serine phosphorylation / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA複製 / chromosome, telomeric region / Ub-specific processing proteases / エンドソーム / クロマチンリモデリング / 細胞分裂 / protein domain specific binding / protein phosphorylation / DNA修復 / protein serine kinase activity / 中心体 / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding 類似検索 - 分子機能 | |||||||||
生物種 | HOMO SAPIENS (ヒト) SYNTHETIC CONSTRUCT (人工物) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å | |||||||||
データ登録者 | Cook, A. / Lowe, E.D. / Chrysina, E.D. / Skamnaki, V.T. / Oikonomakos, N.G. / Johnson, L.N. | |||||||||
引用 | ジャーナル: Biochemistry / 年: 2002 タイトル: Structural Studies on Phospho-Cdk2/Cyclin a Bound to Nitrate, a Transition State Analogue: Implications for the Protein Kinase Mechanism 著者: Cook, A. / Lowe, E.D. / Chrysina, E.D. / Skamnaki, V.T. / Oikonomakos, N.G. / Johnson, L.N. #1: ジャーナル: Nat.Cell Biol. / 年: 1999 タイトル: The Structural Basis for Specificity of Substrate and Recruitment Peptides Fo Cyclin-Dependent Kinases 著者: Brown, N.R. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N. | |||||||||
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 | 1gy3.cif.gz | 240.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1gy3.ent.gz | 192.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1gy3.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/gy/1gy3 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/1gy3 | HTTPS FTP |
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-関連構造データ
関連構造データ | 1qmzS 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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2 |
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper: (Code: given Matrix: (0.99995, 0.00733, -0.00605), ベクター: |
-要素
-タンパク質 , 2種, 4分子 ACBD
#1: タンパク質 | 分子量: 34143.547 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: PHOSPHORYLATED ON THR160 / 由来: (組換発現) HOMO SAPIENS (ヒト) 解説: CDK2 WAS CO-EXPRESSED WITH CAK1 - PRODUCE THR160-PHOSPHO-CDK2 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): B834 (DE3) PLYSS / 参照: UniProt: P24941 #2: タンパク質 | 分子量: 29624.297 Da / 分子数: 2 / Fragment: RESIDUES 175-432 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): B834 (DE3) PLYSS / 参照: UniProt: P20248 |
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-タンパク質・ペプチド , 1種, 2分子 EF
#3: タンパク質・ペプチド | 分子量: 835.953 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: SEQUENCE HHASPRK / 由来: (合成) SYNTHETIC CONSTRUCT (人工物) |
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-非ポリマー , 5種, 170分子
#4: 化合物 | #5: 化合物 | #6: 化合物 | #7: 化合物 | #8: 水 | ChemComp-HOH / | |
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-詳細
配列の詳細 | VAL B 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED IN EXPRESSION CONSTRUCT VAL D 175, N- ...VAL B 175, N-TERMINAL DELETION OF RESIDUES 1-174 ENGINEERED |
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-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: 3.3 Å3/Da / 溶媒含有率: 64.51 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法 / pH: 7 詳細: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 4C FROM SOLUTIONS CONTAINING 10 MG/ML PCDK2/CYCLIN A, 100 MM HEPES PH7.0, 2 MM SUBSTRATE PEPTIDE, 1MM ADP, 1.0 M LI2SO4. CRYSTALS WERE TRANSFERRED ...詳細: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 4C FROM SOLUTIONS CONTAINING 10 MG/ML PCDK2/CYCLIN A, 100 MM HEPES PH7.0, 2 MM SUBSTRATE PEPTIDE, 1MM ADP, 1.0 M LI2SO4. CRYSTALS WERE TRANSFERRED TO 20%PEG 8K, 100 MM HEPES PH 7.0, 10 MM SUBSSTRATE PEPTIDE, 5 MM MG(NO3)2 | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / 手法: 蒸気拡散法, シッティングドロップ法 | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID14-2 / 波長: 0.934 |
検出器 | タイプ: MARRESEARCH / 検出器: CCD |
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: 0.934 Å / 相対比: 1 |
反射 | 解像度: 2.7→20 Å / Num. obs: 45572 / % possible obs: 84.4 % / 冗長度: 7 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 4.2 |
反射 シェル | 解像度: 2.7→2.81 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.5 / % possible all: 40.7 |
反射 | *PLUS 最低解像度: 20 Å / Num. measured all: 319218 |
反射 シェル | *PLUS % possible obs: 40.7 % |
-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: 1QMZ 解像度: 2.7→20 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / ESU R Free: 0.42
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精密化ステップ | サイクル: LAST / 解像度: 2.7→20 Å
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精密化 | *PLUS 最低解像度: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.25 / Rfactor Rwork: 0.25 | ||||||||||||||||||||
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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