- PDB-7kyz: Solution structures of full-length K-RAS bound to GDP -
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基本情報
登録情報
データベース: PDB / ID: 7kyz
タイトル
Solution structures of full-length K-RAS bound to GDP
要素
Isoform 2B of GTPase KRas
キーワード
CELL CYCLE
機能・相同性
機能・相同性情報
forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / protein-membrane adaptor activity / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / positive regulation of glial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / homeostasis of number of cells within a tissue / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / RAF activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / MAP2K and MAPK activation / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / visual learning / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / RAS processing / Signaling by CSF1 (M-CSF) in myeloid cells / Negative regulation of MAPK pathway / 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 / GDP binding / Signaling by BRAF and RAF1 fusions / MAPK cascade / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / G protein activity / actin cytoskeleton organization / Ca2+ pathway / RAF/MAP kinase cascade / neuron apoptotic process / negative regulation of neuron apoptotic process / gene expression / Ras protein signal transduction / mitochondrial outer membrane / Golgi membrane / focal adhesion / GTPase activity 類似検索 - 分子機能
Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
0.7-0.9 mM [U-100% 15N] GTPase KRas, 20 mM [U-2H] MES, 100 mM potassium chloride, 50 mM sodium chloride, 2 mM MgCl2, 1 mM [U-2H] TCEP, 7 mM [U-2H] D2O, 0.05 % sodium azide, 90% H2O/10% D2O
0.7-0.9 mM sample was treated with 2.5% of DMSO to match equal composition of a separate sample that was treated with small-molecule cysteine inhibitor in DMSO. Sample was subsequently purified using Liquid Chromatography (FPLC) system.
15N_sample
90% H2O/10% D2O
solution
3
0.7-0.9 mM [U-13C; U-15N] GTPase KRas, 20 mM [U-2H] MES, 100 mM potassium chloride, 50 mM sodium chloride, 2 mM MgCl2, 1 mM [U-2H] TCEP, 7 mM [U-2H] D2O, 0.05 % sodium azide, 90% H2O/10% D2O
0.7-0.9 mM sample was treated with 2.5% of DMSO to match equal composition of a separate sample that was treated with small-molecule cysteine inhibitor in DMSO. Sample was subsequently purified using Liquid Chromatography (FPLC) system.
13C15N_sample
90% H2O/10% D2O
試料
濃度 (mg/ml)
単位
構成要素
Isotopic labeling
Conc. range (mg/ml)
Solution-ID
20mM
MES
[U-2H]
2
100mM
potassiumchloride
naturalabundance
2
50mM
sodiumchloride
naturalabundance
2
2mM
MgCl2
naturalabundance
2
1mM
TCEP
[U-2H]
2
7mM
D2O
[U-2H]
2
0.05 %
sodiumazide
naturalabundance
2
20mM
MES
[U-2H]
3
100mM
potassiumchloride
naturalabundance
3
50mM
sodiumchloride
naturalabundance
3
2mM
MgCl2
naturalabundance
3
1mM
TCEP
[U-2H]
3
7mM
D2O
[U-2H]
3
0.05 %
sodiumazide
naturalabundance
3
mM
GTPaseKRas
[U-13C; U-15N]
0.7-0.9
3
mM
GTPaseKRas
[U-100% 15N]
0.7-0.9
2
試料状態
詳細: Samples were freshly prepared in NMR buffer pH 6.5. NMR Data was collected with 320 uL sample volume at 298K. Sample apparently held the concentration during the week long data acquisition ...詳細: Samples were freshly prepared in NMR buffer pH 6.5. NMR Data was collected with 320 uL sample volume at 298K. Sample apparently held the concentration during the week long data acquisition with one sample. Two 13C15N labeled NMR samples and one 15N labeled NMR sample was used for all data collection. イオン強度: 0.15 M / Label: conditions_1 / pH: 6.5 / 圧: 1 atm / 温度: 298 K
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NMR測定
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
詳細
Bruker AVANCE III HD
Bruker
AVANCEIIIHD
800
1
TS3.5.6
Bruker AVANCE
Bruker
AVANCE
900
2
TS2.1.6
Bruker AVANCE III
Bruker
AVANCEIII
700
3
TS3.5.6
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解析
NMR software
名称
バージョン
開発者
分類
TopSpin
4
BrukerBiospin
collection
NMRPipe
10.9
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
解析
CcpNmr Analysis
2.4
CCPN
chemicalshiftassignment
PONDEROSA
LeeW, PetitCM, CornilescuG, StarkJL, MarkleyJL.
peakpicking
CYANA
3.98.13
Guntert, MumenthalerandWuthrich
精密化
PONDEROSA
LeeW, PetitCM, CornilescuG, StarkJL, MarkleyJL.
精密化
CYANA
3.98.13
Guntert, MumenthalerandWuthrich
structurecalculation
精密化
手法: torsion angle dynamics / ソフトェア番号: 4 詳細: structures are based on 2140 distance restraints, 138 hydrogen bond restraints as deduced from secondary structure and the tertiary fold detremined using refinement process, and 238 dihedral angle restraints
代表構造
選択基準: target function
NMRアンサンブル
コンフォーマー選択の基準: target function / 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: 20