+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1n4p | ||||||
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タイトル | Protein Geranylgeranyltransferase type-I Complexed with Geranylgeranyl Diphosphate | ||||||
要素 |
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キーワード | TRANSFERASE / protein geranylgeranyltransferase type-I / GGTase / geranylgeranyl / protein prenylation / CaaX / lipid modification / rap2b | ||||||
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 / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / 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 / negative regulation of nitric-oxide synthase biosynthetic process / forebrain astrocyte development / microtubule associated complex / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / heterocyclic compound binding / enzyme-linked receptor protein signaling pathway / Rac protein signal transduction / positive regulation of nitric-oxide synthase biosynthetic process / skeletal muscle cell differentiation / 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 / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / alpha-tubulin binding / SHC1 events in ERBB4 signaling / : / Signalling to RAS / SHC-related events triggered by IGF1R / glial cell proliferation / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / positive regulation of cell cycle / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / response to cytokine / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / response to organic cyclic compound 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.65 Å | ||||||
データ登録者 | Taylor, J.S. / Reid, T.S. / Casey, P.J. / Beese, L.S. | ||||||
引用 | ジャーナル: EMBO J. / 年: 2003 タイトル: Structure of mammalian protein geranylgeranyltransferase type-I 著者: Taylor, J.S. / Reid, T.S. / Terry, K.L. / 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 | 1n4p.cif.gz | 810.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1n4p.ent.gz | 667.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1n4p.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 | 1n4p_validation.pdf.gz | 2.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1n4p_full_validation.pdf.gz | 2.3 MB | 表示 | |
XML形式データ | 1n4p_validation.xml.gz | 148.9 KB | 表示 | |
CIF形式データ | 1n4p_validation.cif.gz | 203.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/n4/1n4p ftp://data.pdbj.org/pub/pdb/validation_reports/n4/1n4p | HTTPS FTP |
-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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-要素
-タンパク質 , 2種, 12分子 ACEGIKBDFHJL
#1: タンパク質 | 分子量: 44098.145 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Fnta / プラスミド: ATCC 63134 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I #2: タンパク質 | 分子量: 42466.176 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Pggt1b / プラスミド: ATCC 63134 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P53610, protein geranylgeranyltransferase type I |
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-タンパク質・ペプチド , 1種, 2分子 MN
#3: タンパク質・ペプチド | 分子量: 1280.685 Da / 分子数: 2 / 由来タイプ: 合成 詳細: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE GERANYLGERANYL LIPID WAS ADDED BY THE ENZYME. 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01116*PLUS |
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-非ポリマー , 5種, 1047分子
#4: 化合物 | ChemComp-ZN / #5: 化合物 | ChemComp-CL / #6: 化合物 | ChemComp-GRG / #7: 化合物 | #8: 水 | ChemComp-HOH / | |
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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: 5.48 Å3/Da / 溶媒含有率: 77.38 % | ||||||||||||||||||||||||||||||||||||||||||
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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: 6.3 詳細: ammonium sulfate, sodium citrate, dithiothreitol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 17 ℃ / 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: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 14-BM-C / 波長: 0.9 Å |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2002年4月19日 / 詳細: Bent conical Si-mirror (Rh coating) |
放射 | モノクロメーター: Bent Ge(111) / 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: 0.9 Å / 相対比: 1 |
反射 | 解像度: 2.65→29.92 Å / Num. all: 286863 / Num. obs: 286863 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 3.6 % / Biso Wilson estimate: 60.8 Å2 / Rsym value: 0.077 / Net I/σ(I): 14 |
反射 シェル | 解像度: 2.65→2.74 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.5 / % possible all: 91.5 |
反射 | *PLUS 最低解像度: 30 Å / Num. measured all: 1038571 / Rmerge(I) obs: 0.077 |
反射 シェル | *PLUS % possible obs: 91.5 % / Rmerge(I) obs: 0.5 |
-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 / 解像度: 2.65→29.92 Å / Rfactor Rfree error: 0.002 / 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 / 詳細: ncs restraints employed during refinement
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 51.0629 Å2 / ksol: 0.374513 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 53.7 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: 2.65→29.92 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.65→2.82 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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精密化 | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 Rfactor Rfree: 0.369 / Rfactor Rwork: 0.344 |