+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1fyr | ||||||
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タイトル | DIMER FORMATION THROUGH DOMAIN SWAPPING IN THE CRYSTAL STRUCTURE OF THE GRB2-SH2 AC-PYVNV COMPLEX | ||||||
要素 |
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キーワード | HORMONE/GROWTH FACTOR / Grb2 / SH2 domain (SH2ドメイン) / phosphopeptide / Met / domain swapping / dimerization / HORMONE-GROWTH FACTOR COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 : / Signaling by FGFR3 fusions in cancer / : / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / : / hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation ...: / Signaling by FGFR3 fusions in cancer / : / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / : / hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / branching involved in labyrinthine layer morphogenesis / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / semaphorin receptor activity / positive regulation of endothelial cell chemotaxis / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / 膵臓 / Interleukin-15 signaling / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Costimulation by the CD28 family / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / Regulation of KIT signaling / epidermal growth factor receptor binding / branching morphogenesis of an epithelial tube / positive chemotaxis / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / negative regulation of thrombin-activated receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / regulation of MAPK cascade / semaphorin-plexin signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / PI3K events in ERBB2 signaling / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / insulin receptor substrate binding / PI3K Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / establishment of skin barrier / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / 食作用 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / MECP2 regulates neuronal receptors and channels / Erythropoietin activates RAS / signal transduction in response to DNA damage / FRS-mediated FGFR3 signaling / positive regulation of microtubule polymerization / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / 髄鞘 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å | ||||||
データ登録者 | Schiering, N. / Casale, E. / Caccia, P. / Giordano, P. / Battistini, C. | ||||||
引用 | ジャーナル: Biochemistry / 年: 2000 タイトル: Dimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex. 著者: Schiering, N. / Casale, E. / Caccia, P. / Giordano, P. / Battistini, C. | ||||||
履歴 |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Please note it has not been proven that the domain- swapped dimer has biological significance. |
-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 | 1fyr.cif.gz | 99.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1fyr.ent.gz | 77 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1fyr.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/fy/1fyr ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyr | HTTPS FTP |
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-関連構造データ
関連構造データ | 1griS S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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2 |
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3 |
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4 |
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5 |
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6 |
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単位格子 |
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詳細 | Dimer 1 is formed from chain I and chain J related by NCS (physiological role not demonstrated) / Dimer 2 is formed from chain K and chain L related by NCS (physiological role not demonstrated) |
-要素
#1: タンパク質 | 分子量: 13281.041 Da / 分子数: 4 / 断片: SH2 DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PGEX-2T / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P29354, UniProt: P62993*PLUS #2: タンパク質・ペプチド | 分子量: 599.570 Da / 分子数: 4 / 断片: RESIDUES 1356-1359 (RESIDUES 0-3 IN COORDINATES) / 由来タイプ: 合成 詳細: The peptide was chemically synthesized. The sequence occurs naturally in humans. 参照: UniProt: P08581 #3: 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: 2 |
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-試料調製
結晶 | マシュー密度: 2.7 Å3/Da / 溶媒含有率: 54 % | ||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.7 詳細: 11% PEG 3350, 0.5M NaCL, 0.1M MES/NaOH pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 20 ℃ | ||||||||||||||||||||||||||||||||||||
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: ELETTRA / ビームライン: 5.2R / 波長: 1 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1996年4月14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: 2.4→20 Å / Num. all: 22423 / Num. obs: 22423 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / 冗長度: 6.3 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.8 |
反射 シェル | 解像度: 2.4→2.58 Å / Rmerge(I) obs: 0.252 / % possible all: 97.7 |
反射 | *PLUS Num. measured all: 140468 |
反射 シェル | *PLUS % possible obs: 97.7 % |
-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 開始モデル: 1GRI 解像度: 2.4→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: mask / Bsol: 30.84 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 36.8 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: 2.4→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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ソフトウェア | *PLUS 名称: CNX / 分類: refinement | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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