+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 6mf0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Crystal Structure Determination of Human/Porcine Chimera Coagulation Factor VIII | |||||||||
![]() | Coagulation factor VIII chimera | |||||||||
![]() | BLOOD CLOTTING / Hemostasis / Hemophilia A / Factor VIII / Chimera | |||||||||
機能・相同性 | ![]() Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant ...Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Defective F8 binding to von Willebrand factor / blood coagulation, intrinsic pathway / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Defective F8 cleavage by thrombin / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Golgi lumen / blood coagulation / Platelet degranulation / signaling receptor activity / oxidoreductase activity / copper ion binding / endoplasmic reticulum lumen / extracellular space / extracellular region / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Smith, I.W. / Spiegel, P.C. | |||||||||
資金援助 | ![]()
| |||||||||
![]() | ![]() タイトル: The 3.2 angstrom structure of a bioengineered variant of blood coagulation factor VIII indicates two conformations of the C2 domain. 著者: Smith, I.W. / d'Aquino, A.E. / Coyle, C.W. / Fedanov, A. / Parker, E.T. / Denning, G. / Spencer, H.T. / Lollar, P. / Doering, C.B. / Spiegel Jr., P.C. #1: ジャーナル: Acta Crystallogr. D Biol. Crystallogr. / 年: 2012 タイトル: Towards automated crystallographic structure refinement with phenix.refine. 著者: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: ジャーナル: Acta Crystallogr D Biol Crystallogr / 年: 2010 タイトル: PHENIX: a comprehensive Python-based system for macromolecular structure solution. 著者: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...著者: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / ![]() 要旨: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | |||||||||
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 | ![]() | 544.8 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 424.8 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 | ![]() | 2.4 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 2.5 MB | 表示 | |
XML形式データ | ![]() | 98.3 KB | 表示 | |
CIF形式データ | ![]() | 132.5 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 |
| ||||||||||||
2 | ![]()
| ||||||||||||
単位格子 |
|
-
要素
-タンパク質 , 1種, 2分子 AB
#1: タンパク質 | 分子量: 168287.047 Da / 分子数: 2 断片: UNP residues 1-386 (pig), 387-761 (human), 762-771,1438-1820 (pig), 2039-2351 (human) 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() ![]() 遺伝子: F8, CF8, F8, F8C 発現宿主: ![]() ![]() 参照: UniProt: P12263, UniProt: P00451 |
---|
-糖 , 4種, 6分子
#2: 多糖 | #3: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | #5: 多糖 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | |
---|
-非ポリマー , 4種, 12分子 ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CU1.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CU1.gif)
![](data/chem/img/HOH.gif)
#6: 化合物 | #7: 化合物 | #8: 化合物 | #9: 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: 2.85 Å3/Da / 溶媒含有率: 56.84 % |
---|---|
結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: 16% PEG3350, 0.025 M magnesium chloride, 0.025 M HEPES |
-データ収集
回折 | 平均測定温度: 80 K / Serial crystal experiment: N |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2014年6月25日 |
放射 | モノクロメーター: single crystal, cylindrically bent Si(220) 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: 0.977408 Å / 相対比: 1 |
反射 | 解像度: 3.198→49.0266 Å / Num. obs: 62358 / % possible obs: 99.85 % / 冗長度: 2 % / Biso Wilson estimate: 62.6319411373 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.1098 / Rpim(I) all: 0.1098 / Rrim(I) all: 0.1552 / Net I/σ(I): 7.3 |
反射 シェル | 解像度: 3.2→3.25 Å / Rmerge(I) obs: 0.6483 / CC1/2: 0.542 / Rpim(I) all: 0.6483 / Rrim(I) all: 0.9168 |
-
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 2R7E 解像度: 3.19999885698→49.0265797404 Å / SU ML: 0.503278702118 / 交差検証法: FREE R-VALUE / σ(F): 1.33786826096 / 位相誤差: 29.7856692332
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 61.4216233514 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3.19999885698→49.0265797404 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル |
|