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基本情報

登録情報
データベース: PDB / ID: 1xr0
タイトルStructural Basis of SNT PTB Domain Interactions with Distinct Neurotrophic Receptors
要素
  • Basic fibroblast growth factor receptor 1
  • FGFR signalling adaptor SNT-1
キーワードSIGNALING PROTEIN/GROWTH FACTOR RECEPTOR / FGFR / SNT / phosphotyrosine binding domain / PTB / TRK / NPXpY motif / SIGNALING PROTEIN-GROWTH FACTOR RECEPTOR COMPLEX
機能・相同性
機能・相同性情報


lens placode formation involved in camera-type eye formation / cell surface receptor protein tyrosine phosphatase signaling pathway / negative regulation of cardiac muscle cell differentiation / lens fiber cell development / Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process ...lens placode formation involved in camera-type eye formation / cell surface receptor protein tyrosine phosphatase signaling pathway / negative regulation of cardiac muscle cell differentiation / lens fiber cell development / Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / anterior/posterior axis specification, embryo / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / cementum mineralization / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / response to sodium phosphate / auditory receptor cell development / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / chordate embryonic development / positive regulation of parathyroid hormone secretion / mesenchymal cell proliferation / fibroblast growth factor receptor binding / phosphatase activator activity / paraxial mesoderm development / regulation of postsynaptic density assembly / FGFR1b ligand binding and activation / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / neurotrophin TRKA receptor binding / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of epithelial cell proliferation / gastrulation with mouth forming second / outer ear morphogenesis / embryonic limb morphogenesis / positive regulation of vascular endothelial cell proliferation / RND1 GTPase cycle / positive regulation of endothelial cell chemotaxis / skeletal system morphogenesis / RND2 GTPase cycle / positive regulation of mesenchymal cell proliferation / middle ear morphogenesis / ventricular septum development / ureteric bud development / cardiac muscle cell proliferation / inner ear morphogenesis / Signaling by ALK / PI-3K cascade:FGFR3 / Frs2-mediated activation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / PI-3K cascade:FGFR2 / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / midbrain development / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / fibroblast growth factor binding / regulation of cell differentiation / RET signaling / PI3K Cascade / cellular response to fibroblast growth factor stimulus / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / epithelial to mesenchymal transition / chondrocyte differentiation / Activated NTRK2 signals through FRS2 and FRS3 / regulation of ERK1 and ERK2 cascade / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / calcium ion homeostasis / cell maturation / forebrain development / FRS-mediated FGFR3 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / positive regulation of MAP kinase activity / endomembrane system / positive regulation of neuron differentiation / SH2 domain binding
類似検索 - 分子機能
FRS2, PTB domain / : / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Fibroblast growth factor receptor 1, catalytic domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Fibroblast growth factor receptor family / Immunoglobulin ...FRS2, PTB domain / : / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Fibroblast growth factor receptor 1, catalytic domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
類似検索 - ドメイン・相同性
Fibroblast growth factor receptor 1 / Fibroblast growth factor receptor substrate 2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法溶液NMR / Structures of the SNT-1 PTB domain in complex with the hFGFR1 peptide were calculated with a distance geometry, simulated annealing protocol by using the X-PLOR program ([4]). NOE distance, dihedral angle restraints were treated with a square-well potential of 50 kcal mol?1 ?2. A total of 2448 manually assigned NOE-derived distance restraints were obtained from the 15N- or 13C-edited NOESY data. Included in this figure are 251 intrapeptide, 258 intermolecular distance restraints. Additionally, 255 unambiguous, 52 ambiguous distance restraints were identified from the NOE data by using ARIA. The final structure calculations employed a total of 2755 NOE restraints obtained from the manual, the ARIA-assisted assignments, 2703 of which were unambiguously assigned NOE-derived distance restraints that comprise 1072 intraresidue, 466 sequential, 216 medium-range, and 949 long-range NOEs. In addition, 70 hydrogen-bond distance restraints for 35 hydrogen bonds, 19 -angle restraints were also used in the structure calculations. For the ensemble of the final 20 structures, no distance or torsional angle restraint was violated by more than 0.4 or 5, respectively. The distance-violation, dihedral-violation, and total energies were 74.4 1.7 kcal mol, 1, 0.82 0.08 kcal mol, 1, and 262.0 6.0 kcal mol, 1, respectively. The Lennard-Jones potential, which was not used during any refinement stage, was 659.3 23.1 kcal mol, 1 for the final structures. Ramachandran plot analysis by Procheck-NMR showed that in the final structures of the complex, 98.1% of the backbone geometries of the non-Gly, non-Pro residues in the complex (protein residues 18-116, peptide residues (412-430), nearly 100% in the secondary structure (protein residues 19-24, 35-40, 45-49, 52-57, 63-68, 71-76, 85-90, 94-107, and 111-115, peptide residues 426-430) lie within energetically favorable or allowed regions.
データ登録者Dhalluin, C. / Yan, K.S. / Plotnikova, O. / Lee, K.W. / Zeng, L. / Kuti, M. / Mujtaba, S. / Goldfarb, M.P. / Zhou, M.-M.
引用ジャーナル: Mol.Cell / 年: 2000
タイトル: Structural Basis of SNT PTB Domain Interactions with Distinct Neurotrophic Receptors
著者: Dhalluin, C. / Yan, K.S. / Plotnikova, O. / Lee, K.W. / Zeng, L. / Kuti, M. / Mujtaba, S. / Goldfarb, M.P. / Zhou, M.-M.
履歴
登録2004年10月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02004年11月2日Provider: repository / タイプ: Initial release
改定 1.12008年4月30日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32022年3月2日Group: Database references / Derived calculations
カテゴリ: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
改定 1.42024年5月22日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Basic fibroblast growth factor receptor 1
B: FGFR signalling adaptor SNT-1


分子量 (理論値)分子数
合計 (水以外)17,4992
ポリマ－17,4992
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)1 / 100structures with the least restraint violations
代表モデルfewest violations

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要素

#1: タンパク質・ペプチド Basic fibroblast growth factor receptor 1 / FGFR-1 / bFGF-R / Fms-like tyrosine kinase-2 / c-fgr


分子量: 2492.983 Da / 分子数: 1
断片: Sequence database residues 409-430 from the juxtamembrane region of hFGFR1
由来タイプ: 合成
詳細: The peptide was chemically synthesized. The sequence is taken from Homo sapiens (human).
参照: UniProt: P11362
#2: タンパク質 FGFR signalling adaptor SNT-1


分子量: 15005.791 Da / 分子数: 1 / 断片: PTB domain at the N terminus / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8WU20

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実験情報

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実験

実験手法: 溶液NMR
NMR実験
Conditions-IDExperiment-IDSolution-IDタイプ
111HNHA
1213D 13C-separated NOESY
1313D 15N-separated NOESY
1412D NOESY
NMR実験の詳細Text: NMR spectra were acquired at 30C on a Bruker DRX600 or DRX500 spectrometer. The backbone and side chain 1H, 13C, and 15N resonances of the protein were assigned using deuterium-decoupled triple- ...Text: NMR spectra were acquired at 30C on a Bruker DRX600 or DRX500 spectrometer. The backbone and side chain 1H, 13C, and 15N resonances of the protein were assigned using deuterium-decoupled triple-resonance experiments of HNCA, HN(CO)CA, HNCACB, HN(CO)CACB, and (H)C(CO)NH-TOCSY ([34 and 30]) recorded by using uniformly 15N/13C-labeled and fractionally deuterated protein in complex with a nonisotopically labeled hFGFR1 peptide. The side chain assignments were completed using 3D HCCH-TOCSY ([7]) data collected from a uniformly 15N/13C labeled-protein/nonlabeled-peptide complex. NOE-derived distance restraints were obtained from 15N- or 13C-edited 3D NOESY spectra ([7]). -angle restraints were determined from 3JHN,H coupling constants measured in a 3D HNHA-J spectrum ([7]). Slowly exchanging amide protons were identified from a series of 2D 15N-HSQC spectra recorded after the H2O buffer was changed to 2H2O buffer. The peptide resonances were assigned using 13C/15N-filtered 2D NOESY and TOCSY spectra ([30]) collected from a 15N/13C labeled-protein/nonlabeled-peptide complex. The intermolecular NOEs used in defining the structure of the SNT-1 PTB domain/hFGFR1 complex were detected in 13C- or 15N-edited (F 1), 13C/15N-filtered (F 3) 3D NOESY spectra. All NMR spectra were processed with NMRPipe/NMRDraw ([8]) and analyzed using NMRView.

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試料調製

詳細内容: SNT-1 PTB domain/hFGFR1 peptide complex (1:1) of ~0.5 mM in 100 mM phosphate buffer of pH 6.5, 5 mM DTT-d10, and 0.5 mM EDTA in H2O/2H2O (9/1) or 2H2O
溶媒系: H2O/2H2O (9/1) or 100% 2H2O
試料状態イオン強度: 15 mM DTT-d10, and 0.5 mM EDTA00 mM phosphate buffer,
pH: 6.5 / 圧: 1 atm / 温度: 303 K

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NMR測定

放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M
放射波長相対比: 1
NMRスペクトロメーター
タイプ製造業者モデル磁場強度 (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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解析

NMR software
名称バージョン開発者分類
X-PLOR3.851Brunger構造決定
ARIA1.1M. Nilges and S. O'Donoghue精密化
精密化手法: Structures of the SNT-1 PTB domain in complex with the hFGFR1 peptide were calculated with a distance geometry, simulated annealing protocol by using the X-PLOR program ([4]). NOE distance, ...手法: Structures of the SNT-1 PTB domain in complex with the hFGFR1 peptide were calculated with a distance geometry, simulated annealing protocol by using the X-PLOR program ([4]). NOE distance, dihedral angle restraints were treated with a square-well potential of 50 kcal mol?1 ?2. A total of 2448 manually assigned NOE-derived distance restraints were obtained from the 15N- or 13C-edited NOESY data. Included in this figure are 251 intrapeptide, 258 intermolecular distance restraints. Additionally, 255 unambiguous, 52 ambiguous distance restraints were identified from the NOE data by using ARIA. The final structure calculations employed a total of 2755 NOE restraints obtained from the manual, the ARIA-assisted assignments, 2703 of which were unambiguously assigned NOE-derived distance restraints that comprise 1072 intraresidue, 466 sequential, 216 medium-range, and 949 long-range NOEs. In addition, 70 hydrogen-bond distance restraints for 35 hydrogen bonds, 19 -angle restraints were also used in the structure calculations. For the ensemble of the final 20 structures, no distance or torsional angle restraint was violated by more than 0.4 or 5, respectively. The distance-violation, dihedral-violation, and total energies were 74.4 1.7 kcal mol, 1, 0.82 0.08 kcal mol, 1, and 262.0 6.0 kcal mol, 1, respectively. The Lennard-Jones potential, which was not used during any refinement stage, was 659.3 23.1 kcal mol, 1 for the final structures. Ramachandran plot analysis by Procheck-NMR showed that in the final structures of the complex, 98.1% of the backbone geometries of the non-Gly, non-Pro residues in the complex (protein residues 18-116, peptide residues (412-430), nearly 100% in the secondary structure (protein residues 19-24, 35-40, 45-49, 52-57, 63-68, 71-76, 85-90, 94-107, and 111-115, peptide residues 426-430) lie within energetically favorable or allowed regions.
ソフトェア番号: 1
代表構造選択基準: fewest violations
NMRアンサンブルコンフォーマー選択の基準: structures with the least restraint violations
計算したコンフォーマーの数: 100 / 登録したコンフォーマーの数: 1

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