+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2fib | ||||||
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タイトル | RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) COMPLEXED TO THE PEPTIDE GLY-PRO-ARG-PRO AT PH 6.0 | ||||||
要素 |
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キーワード | COMPLEX (BLOOD COAGULATION/PEPTIDE) / FIBRINOGEN (フィブリノゲン) / BLOOD COAGULATION (凝固・線溶系) / FIBRIN POLYMERIZATION / COMPLEX (BLOOD COAGULATION-PEPTIDE) / COMPLEX (BLOOD COAGULATION-PEPTIDE) complex | ||||||
機能・相同性 | 機能・相同性情報 platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / Α顆粒 / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane ...platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / Α顆粒 / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of exocytosis / positive regulation of peptide hormone secretion / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / protein polymerization / Integrin cell surface interactions / cellular response to interleukin-1 / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / fibrinolysis / cell adhesion molecule binding / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 血小板 / response to calcium ion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / blood microparticle / positive regulation of ERK1 and ERK2 cascade / external side of plasma membrane / 小胞体 / signaling receptor binding / structural molecule activity / 細胞膜 / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / ISOMORPHOUS WITH PDB ENTRY 1FIB / 解像度: 2.01 Å | ||||||
データ登録者 | Pratt, K.P. / Cote, H.C.F. / Chung, D.W. / Stenkamp, R.E. / Davie, E.W. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1997 タイトル: The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro. 著者: Pratt, K.P. / Cote, H.C. / Chung, D.W. / Stenkamp, R.E. / Davie, E.W. | ||||||
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 | 2fib.cif.gz | 63.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2fib.ent.gz | 47.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2fib.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/fi/2fib ftp://data.pdbj.org/pub/pdb/validation_reports/fi/2fib | 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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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 30243.422 Da / 分子数: 1 断片: GAMMA CHAIN, CARBOXYL TERMINAL FRAGMENT RESIDUES 143 - 411 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 組織: BLOOD PLASMA血漿 遺伝子: HUMAN FIBRINOGEN GAMMA CHAIN CDNA ENCODING VAL 143 - VAL 411 器官: BLOOD血液 / プラスミド: PPIC9K / 発現宿主: Pichia pastoris (菌類) / 参照: UniProt: P02679 |
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#2: タンパク質・ペプチド | 分子量: 426.490 Da / 分子数: 1 / 由来タイプ: 組換発現 |
#3: 化合物 | ChemComp-CA / |
#4: 水 | ChemComp-HOH / |
配列の詳細 | NO DENSITY FOR RESIDUES BEYOND LEU 392 WAS OBSERVED. MASS SPECTROMET |
-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: 1.91 Å3/Da / 溶媒含有率: 35.52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 詳細: PROTEIN WAS CRYSTALLIZED FROM 12% PEG8000, 70MM CACL2, 0.1 M MES, PH 6.0, 0.02%NAN3, ROOM TEMPERATURE, SITTING DROPS. THE CRYSTAL WAS SOAKED OVERNIGHT IN THE ORIGINAL SOLUTION PLUS 0.01M GLY- ...詳細: PROTEIN WAS CRYSTALLIZED FROM 12% PEG8000, 70MM CACL2, 0.1 M MES, PH 6.0, 0.02%NAN3, ROOM TEMPERATURE, SITTING DROPS. THE CRYSTAL WAS SOAKED OVERNIGHT IN THE ORIGINAL SOLUTION PLUS 0.01M GLY-PRO-ARG-PRO (SIGMA), THEN BACK-SOAKED FOR 10 MINUTES., vapor diffusion - sitting drop Temp details: room temp | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, シッティングドロップ法 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 300 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RUH2R / 波長: 1.5418 |
検出器 | タイプ: RIGAKU / 検出器: IMAGE PLATE / 日付: 1995年9月1日 / 詳細: MIRRORS |
放射 | 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→68.2 Å / Num. obs: 12275 / % possible obs: 76.9 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.054 / Rsym value: 0.052 / Net I/σ(I): 11 |
反射 シェル | 解像度: 2.01→2.25 Å / Mean I/σ(I) obs: 3.17 / % possible all: 61.3 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: ISOMORPHOUS WITH PDB ENTRY 1FIB 開始モデル: PDB ENTRY 1FIB 解像度: 2.01→10 Å / σ(F): 3 詳細: MODIFIED TOPOLOGY AND PARAMETER FILES WERE CREATED SO THAT X-PLOR WOULD ACCEPT A CIS PEPTIDE BOND THAT DID NOT PRECEDE A PROLINE RESIDUE. THE PDB INPUT FILE FOR X-PLOR SHOULD SPECIFY CYS 339 ...詳細: MODIFIED TOPOLOGY AND PARAMETER FILES WERE CREATED SO THAT X-PLOR WOULD ACCEPT A CIS PEPTIDE BOND THAT DID NOT PRECEDE A PROLINE RESIDUE. THE PDB INPUT FILE FOR X-PLOR SHOULD SPECIFY CYS 339 AS CCY 339. THE BACKBONE ANGLES PHI AND PSI OF ASN 337 ARE STRAINED.
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原子変位パラメータ | Biso mean: 23.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.01→10 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→10 Å / Total num. of bins used: 20 /
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Xplor file |
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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