+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1d8d | ||||||
---|---|---|---|---|---|---|---|
タイトル | CO-CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A K-RAS4B PEPTIDE SUBSTRATE AND FPP ANALOG AT 2.0A RESOLUTION | ||||||
要素 |
| ||||||
キーワード | TRANSFERASE (転移酵素) / FTASE / PFT / PFTASE / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / CAAX / RAS / CANCER (悪性腫瘍) | ||||||
機能・相同性 | 機能・相同性情報 Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / enzyme-linked receptor protein signaling pathway / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / positive regulation of nitric-oxide synthase biosynthetic process / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / alpha-tubulin binding / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / response to inorganic substance / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of cell cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / 低分子量GTPアーゼ / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / response to cytokine / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / wound healing / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / lipid metabolic process 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) | ||||||
手法 | X線回折 / 解像度: 2 Å | ||||||
データ登録者 | Long, S.B. / Casey, P.J. / Beese, L.S. | ||||||
引用 | ジャーナル: Structure Fold.Des. / 年: 2000 タイトル: The basis for K-Ras4B binding specificity to protein farnesyltransferase revealed by 2 A resolution ternary complex structures. 著者: Long, S.B. / Casey, P.J. / Beese, L.S. #1: ジャーナル: Science / 年: 1997 タイトル: Crystal Structure of Protein Farnesyltransferase at 2.25A Resolution 著者: Park, H.-W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S. #2: ジャーナル: Biochemistry / 年: 1998 タイトル: Co-crystal Structure of Mammalian Protein Farnesyltransferase with a Farnesyl Diphosphate Substrate 著者: Long, S.B. / Casey, P.J. / Beese, L.S. | ||||||
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 | 1d8d.cif.gz | 173.1 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1d8d.ent.gz | 134.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1d8d.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/d8/1d8d ftp://data.pdbj.org/pub/pdb/validation_reports/d8/1d8d | 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
-Farnesyltransferase ... , 2種, 2分子 AB
#1: タンパク質 | 分子量: 44098.145 Da / 分子数: 1 / 断片: alpha subunit / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 器官: BRAIN脳 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q04631, squalene synthase |
---|---|
#2: タンパク質 | 分子量: 48722.281 Da / 分子数: 1 / 断片: beta subunit / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 器官: BRAIN脳 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q02293, squalene synthase |
-タンパク質・ペプチド , 1種, 1分子 P
#3: タンパク質・ペプチド | 分子量: 1298.723 Da / 分子数: 1 / 由来タイプ: 合成 詳細: This synthetic peptide is derived from human K-Ras4B, residues 178-188. 参照: UniProt: P01116 |
---|
-非ポリマー , 4種, 453分子
#4: 化合物 | ChemComp-ZN / | ||||
---|---|---|---|---|---|
#5: 化合物 | ChemComp-ACT / #6: 化合物 | ChemComp-FII / [( | #7: 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 |
---|
-試料調製
結晶 | マシュー密度: 3.1 Å3/Da / 溶媒含有率: 60.35 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | 温度: 290 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.7 詳細: Peg 8000, ammonium acetate, DTT, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||
結晶化 | *PLUS 温度: 17 ℃ | ||||||||||||||||||||
溶液の組成 | *PLUS
|
-データ収集
回折 | 平均測定温度: 96 K |
---|---|
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: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 1998年10月23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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2→35 Å / Num. all: 77998 / Num. obs: 76088 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / 冗長度: 4.2 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.9 |
反射 シェル | 解像度: 2→2.02 Å / 冗長度: 2.3 % / Rmerge(I) obs: 0.197 / Num. unique all: 2154 / % possible all: 83.9 |
反射 | *PLUS Num. measured all: 320401 |
反射 シェル | *PLUS % possible obs: 83.9 % |
-解析
ソフトウェア |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 解像度: 2→35 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2 / σ(I): -3 / 立体化学のターゲット値: Engh & Huber
| |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 34.2 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2→35 Å
| |||||||||||||||||||||||||
拘束条件 |
| |||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2→2.09 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.851 / 分類: refinement | |||||||||||||||||||||||||
拘束条件 | *PLUS
|