+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1kzp | ||||||
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タイトル | PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A FARNESYLATED K-RAS4B PEPTIDE PRODUCT | ||||||
要素 |
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キーワード | TRANSFERASE/TRANSFERASE SUBSTRATE / FTASE / PFT / PFTASE / FT / FPT / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / FARNESYL PROTEIN TRANSFERASE (ファルネソール) / CAAX / RAS CANCER / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX | ||||||
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 nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / 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 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of cell cycle / 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 / 分子置換 / 解像度: 2.1 Å | ||||||
データ登録者 | Long, S.B. / Casey, P.J. / Beese, L.S. | ||||||
引用 | ジャーナル: Nature / 年: 2002 タイトル: Reaction path of protein farnesyltransferase at atomic resolution 著者: Long, S.B. / Casey, P.J. / Beese, L.S. #1: ジャーナル: Structure / 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. #2: ジャーナル: Science / 年: 1997 タイトル: Crystal Structure of Protein Farnesyltransferase at 2.25 A Resolution 著者: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S. #3: ジャーナル: Biochemistry / 年: 1998 タイトル: Co-Crystal Structure of Protein Farnesyltransferase Complexed with a Farnesyl Diphosphate Substrate 著者: Long, S.B. / Casey, P.J. / Beese, L.S. | ||||||
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 | 1kzp.cif.gz | 172.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1kzp.ent.gz | 133 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1kzp.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/kz/1kzp ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kzp | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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詳細 | The biological unit of protein farnesyltransferase (FTase) is a heterodimer of alpha and beta subunits. There is one FTase heterodimer per asymmetric unit. |
-要素
-Protein Farnesyltransferase ... , 2種, 2分子 AB
#1: タンパク質 | 分子量: 44098.145 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q04631, squalene synthase |
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#2: タンパク質 | 分子量: 48722.281 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) 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 C
#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: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS. 参照: UniProt: P01118, UniProt: P01116*PLUS |
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-非ポリマー , 4種, 425分子
#4: 化合物 | ChemComp-ZN / | ||||
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#5: 化合物 | #6: 化合物 | ChemComp-FAR / | #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 |
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-試料調製
結晶 | マシュー密度: 3.12 Å3/Da / 溶媒含有率: 60.54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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, Magnesium Chloride, DTT, Tris-HCl, pH 5.70, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 17 ℃ / pH: 7 / 詳細: Park, H.W., (1997) Science, 275, 1800. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 回転陽極 / タイプ: RIGAKU RUH3R / 波長: 1.5418 / 波長: 1.5418 Å |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 1999年7月26日 / 詳細: Mirrors |
放射 | モノクロメーター: Ni Filter / 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: 2.1→50 Å / Num. obs: 67840 / % possible obs: 100 % / Observed criterion σ(I): -3 / 冗長度: 5.93 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.086 / Net I/σ(I): 21 |
反射 シェル | 解像度: 2.1→2.12 Å / 冗長度: 5.62 % / Mean I/σ(I) obs: 2.47 / Num. unique all: 2216 / Rsym value: 0.637 / % possible all: 100 |
反射 | *PLUS 最高解像度: 2.1 Å / 最低解像度: 50 Å / % possible obs: 100 % / Num. measured all: 402441 / Rmerge(I) obs: 0.086 |
反射 シェル | *PLUS 最高解像度: 2.1 Å / 最低解像度: 2.2 Å / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.8 |
-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: PDB entry 1D8D 解像度: 2.1→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ | Biso mean: 34.3 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.1→50 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.1→2.2 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
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Xplor file |
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精密化 | *PLUS 最高解像度: 2.1 Å / 最低解像度: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.1659 / Rfactor obs: 0.164 / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.164 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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LS精密化 シェル | *PLUS 最高解像度: 2.1 Å / 最低解像度: 2.2 Å / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.235 |