[English] 日本語
Yorodumi- PDB-2mse: NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mse | ||||||
---|---|---|---|---|---|---|---|
Title | NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered to a lipid-bilayer nanodisc | ||||||
Components |
| ||||||
Keywords | LIPID BINDING PROTEIN / K-Ras / Nanodisc / PRE / Docking / A-RafRBD | ||||||
Function / homology | Function and homology information endocrine signaling / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation ...endocrine signaling / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport / cholesterol import / high-density lipoprotein particle binding / ABC transporters in lipid homeostasis / regulation of proteasomal ubiquitin-dependent protein catabolic process / blood vessel endothelial cell migration / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / peptidyl-methionine modification / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / regulation of TOR signaling / acylglycerol homeostasis / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of cholesterol metabolic process / lipid storage / high-density lipoprotein particle clearance / phospholipid homeostasis / chylomicron / high-density lipoprotein particle remodeling / phospholipid efflux / chemorepellent activity / cholesterol transfer activity / reverse cholesterol transport / very-low-density lipoprotein particle / high-density lipoprotein particle assembly / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / cholesterol transport / high-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / endothelial cell proliferation / forebrain astrocyte development / MAP kinase kinase kinase activity / negative regulation of interleukin-1 beta production / Scavenging by Class A Receptors / cholesterol efflux / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / negative chemotaxis / positive regulation of cholesterol efflux / positive regulation of Rho protein signal transduction / adrenal gland development / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / cholesterol binding / Rac protein signal transduction / cholesterol biosynthetic process / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / positive regulation of glial cell proliferation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / endocytic vesicle / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / EGFR Transactivation by Gastrin / negative regulation of tumor necrosis factor-mediated signaling pathway / SHC1 events in EGFR signaling / Signalling to RAS / GRB2 events in ERBB2 signaling / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC1 events in ERBB2 signaling / Scavenging of heme from plasma / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Mazhab-Jafari, M. / Stathopoulos, P. / Marshall, C. / Ikura, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site. Authors: Mazhab-Jafari, M.T. / Marshall, C.B. / Smith, M.J. / Gasmi-Seabrook, G.M. / Stathopulos, P.B. / Inagaki, F. / Kay, L.E. / Neel, B.G. / Ikura, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2mse.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2mse.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 2mse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mse_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2mse_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 2mse_validation.xml.gz | 536.8 KB | Display | |
Data in CIF | 2mse_validation.cif.gz | 623.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/2mse ftp://data.pdbj.org/pub/pdb/validation_reports/ms/2mse | HTTPS FTP |
-Related structure data
Related structure data | 2mscC 2msdC 2m4a 2m4b C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
-Protein , 3 types, 4 molecules ACBD
#1: Protein | Mass: 23234.295 Da / Num. of mol.: 2 / Fragment: UNP residues 68-265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Plasmid: pGBHPS MSP / Production host: Escherichia coli (E. coli) / References: UniProt: P02647 #2: Protein | | Mass: 21260.250 Da / Num. of mol.: 1 / Fragment: UNP residues 1-185 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, UniProt: A0A024RAV5*PLUS #3: Protein | | Mass: 8133.491 Da / Num. of mol.: 1 / Fragment: UNP residues 19-91 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARAF, ARAF1, PKS, PKS2 / Plasmid: pGEX-4TpGEX-4T22 / Production host: Escherichia coli (E. coli) References: UniProt: P10398, non-specific serine/threonine protein kinase |
---|
-Non-polymers , 4 types, 82 molecules
#4: Chemical | ChemComp-PCW / #5: Chemical | ChemComp-17F / #6: Chemical | ChemComp-GNP / | #7: Chemical | ChemComp-MG / | |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: This is a hybrid model generated by Haddock docking simulation that is based on i) NMR data that includes PRE-measurements between lipids (i.e. nanodisc) and the protien (i.e. K-RasGNP and A- ...Details: This is a hybrid model generated by Haddock docking simulation that is based on i) NMR data that includes PRE-measurements between lipids (i.e. nanodisc) and the protien (i.e. K-RasGNP and A-RafRBD) ii) crystolagraphic information (K-RasGNP and A-RafRBD) and iii) theoretical computation (i.e. nanodisc). | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||
NMR details | Text: All PRE measurements were carrried out on the C-delta of Ile residues. |
-Sample preparation
Details |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
|