+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 5kiw | ||||||
---|---|---|---|---|---|---|---|
タイトル | p97 ND1-L198W in complex with VIMP | ||||||
![]() |
| ||||||
![]() | HYDROLASE/MEMBRANE PROTEIN / p97 adaptor protein / VCP-interacting membrane protein / VIMP / p97 / HYDROLASE-MEMBRANE PROTEIN complex | ||||||
機能・相同性 | ![]() regulation of nitric oxide metabolic process / negative regulation of acute inflammatory response to antigenic stimulus / Derlin-1-VIMP complex / negative regulation of macrophage apoptotic process / negative regulation of glycogen biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / positive regulation of Lys63-specific deubiquitinase activity / very-low-density lipoprotein particle / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation ...regulation of nitric oxide metabolic process / negative regulation of acute inflammatory response to antigenic stimulus / Derlin-1-VIMP complex / negative regulation of macrophage apoptotic process / negative regulation of glycogen biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / positive regulation of Lys63-specific deubiquitinase activity / very-low-density lipoprotein particle / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / negative regulation of glucose import / protein-DNA covalent cross-linking repair / low-density lipoprotein particle / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / aggresome assembly / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein localization to chromatin / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / positive regulation of mitochondrial membrane potential / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of protein localization to chromatin / response to redox state / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / regulation of gluconeogenesis / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ER overload response / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / cytoplasmic microtubule / antioxidant activity / negative regulation of interleukin-6 production / RHOH GTPase cycle / autophagosome maturation / negative regulation of tumor necrosis factor production / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / interstrand cross-link repair / response to glucose / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / viral genome replication / proteasome complex / lipid droplet / Josephin domain DUBs / cell redox homeostasis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / negative regulation of inflammatory response / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / cellular response to insulin stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / Neddylation / site of double-strand break / cellular response to heat / cellular response to oxidative stress / ATPase binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Tang, W.K. / Xia, D. | ||||||
![]() | ![]() タイトル: Structural basis for nucleotide-modulated p97 association with the ER membrane. 著者: Tang, W.K. / Zhang, T. / Ye, Y. / Xia, D. | ||||||
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 | ![]() | 400.1 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 333.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1 MB | 表示 | |
XML形式データ | ![]() | 36.3 KB | 表示 | |
CIF形式データ | ![]() | 48.8 KB | 表示 | |
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域:
NCSアンサンブル:
NCS oper:
|
-
要素
#1: タンパク質 | 分子量: 52388.875 Da / 分子数: 2 / 断片: N-terminal residues 1-460 / 変異: L198W / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 9729.287 Da / 分子数: 2 / 断片: residues 49-122 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #3: 化合物 | #4: 化合物 | #5: 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: 3.7 Å3/Da / 溶媒含有率: 66.73 % |
---|---|
結晶化 | 温度: 288 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 詳細: 0.1 M Tris, pH 8, 15 % ethanol, 100 mM NaCl, 7 % MPD |
-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: RAYONIX MX300HE / 検出器: CCD / 日付: 2014年11月1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 Å / 相対比: 1 |
反射 | 解像度: 3.41→50 Å / Num. obs: 22714 / % possible obs: 95.9 % / 冗長度: 4 % / Net I/σ(I): 11.6 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: 4KO8 解像度: 3.41→49.268 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.852 / SU B: 70.624 / SU ML: 0.489 / 交差検証法: THROUGHOUT / ESU R Free: 0.616 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 134.956 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: 1 / 解像度: 3.41→49.268 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
|