+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 3gj6 | ||||||
---|---|---|---|---|---|---|---|
タイトル | Crystal structure of human RanGDP-Nup153ZnF1 complex | ||||||
![]() |
| ||||||
![]() | TRANSPORT PROTEIN / G protein / GDP / Ran / Nuclear Pore / Nup153 / Zinc Finger / Acetylation / Cytoplasm / GTP-binding / Host-virus interaction / Isopeptide bond / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Protein transport / Transport / Ubl conjugation / DNA-binding / Metal-binding / mRNA transport / Nuclear pore complex / Translocation / Zinc / Zinc-finger | ||||||
機能・相同性 | ![]() nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins ...nucleoplasmic side of nuclear pore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNP Assembly / SUMOylation of ubiquitinylation proteins / Nuclear Pore Complex (NPC) Disassembly / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / Transcriptional regulation by small RNAs / Regulation of Glucokinase by Glucokinase Regulatory Protein / SUMOylation of DNA damage response and repair proteins / negative regulation of RNA export from nucleus / annulate lamellae / Regulation of HSF1-mediated heat shock response / nuclear pore complex assembly / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / nuclear inclusion body / nuclear pore nuclear basket / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / nuclear localization sequence binding / dynein intermediate chain binding / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / mRNA transport / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / protein-membrane adaptor activity / centriole / viral process / protein export from nucleus / nuclear periphery / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / double-stranded DNA binding / nuclear membrane / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Partridge, J.R. / Schwartz, T.U. | ||||||
![]() | ![]() タイトル: Crystallographic and Biochemical Analysis of the Ran-binding Zinc Finger Domain. 著者: Partridge, J.R. / Schwartz, T.U. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 112.8 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 85.2 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | 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 |
| ||||||||
Components on special symmetry positions |
|
-
要素
-タンパク質 / タンパク質・ペプチド , 2種, 2分子 AB
#1: タンパク質 | 分子量: 24846.479 Da / 分子数: 1 / 変異: F35S / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
---|---|
#2: タンパク質・ペプチド | 分子量: 3528.045 Da / 分子数: 1 Fragment: Nup153 - Zinc finger module 1: UNP residues 658-686 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
-非ポリマー , 4種, 37分子 ![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | ChemComp-MG / |
---|---|
#4: 化合物 | ChemComp-GDP / |
#5: 化合物 | ChemComp-ZN / |
#6: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.32 Å3/Da / 溶媒含有率: 47.08 % |
---|---|
結晶化 | 温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 0.1 M Bis-Tris pH 6.5, 18-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2008年8月4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: 0.979 Å / 相対比: 1 |
反射 | 解像度: 2.7→50 Å / Num. all: 7528 / Num. obs: 7528 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 4.6 % / Biso Wilson estimate: 47.33 Å2 / Rsym value: 0.07 / Net I/σ(I): 16.8 |
反射 シェル | 解像度: 2.7→2.8 Å / 冗長度: 4.4 % / Mean I/σ(I) obs: 2.62 / Rsym value: 0.7 / % possible all: 92.3 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: PDB entry 3GJ3 解像度: 2.7→36.116 Å / SU ML: 0.81 / 位相誤差: 32.1 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 48.934 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.7→36.116 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 TLS | Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 TLSグループ | Selection details: Chain B |