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Yorodumi- PDB-4q21: MOLECULAR SWITCH FOR SIGNAL TRANSDUCTION: STRUCTURAL DIFFERENCES ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q21 | ||||||
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Title | MOLECULAR SWITCH FOR SIGNAL TRANSDUCTION: STRUCTURAL DIFFERENCES BETWEEN ACTIVE AND INACTIVE FORMS OF PROTOONCOGENIC RAS PROTEINS | ||||||
Components | C-H-RAS P21 PROTEIN CATALYTIC DOMAIN | ||||||
Keywords | ONCOGENE PROTEIN | ||||||
Function / homology | Function and homology information GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / 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 / SHC1 events in EGFR signaling / positive regulation of protein targeting to membrane / Signalling to RAS / GRB2 events in ERBB2 signaling / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC1 events in ERBB2 signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / positive regulation of epithelial cell proliferation / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / myelination / Signaling by FGFR1 in disease / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / Signaling by ERBB2 TMD/JMD mutants / small monomeric GTPase / positive regulation of MAP kinase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of GTPase activity / VEGFR2 mediated cell proliferation / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Signaling by SCF-KIT / cellular senescence / cellular response to gamma radiation / positive regulation of fibroblast proliferation / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / endocytosis / positive regulation of type II interferon production / 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 / chemotaxis / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Kim, S.-H. | ||||||
Citation | Journal: Science / Year: 1990 Title: Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. Authors: Milburn, M.V. / Tong, L. / deVos, A.M. / Brunger, A. / Yamaizumi, Z. / Nishimura, S. / Kim, S.H. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: X-Ray Crystal Structures of Transforming P21 Ras Mutants Suggest a Transition-State Stabilization Mechanism for GTP Hydrolysis Authors: Prive, G.G. / Milburn, M.V. / Tong, L. / Devos, A.M. / Yamaizumi, Z. / Nishimura, S. / Kim, S.-H. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990 Title: Crystal Structure of an Active Form of Ras Protein, a Complex of a GTP Analog and the Hras P21 Catalytic Domain Authors: Brunger, A.T. / Milburn, M.V. / Tong, L. / Devos, A.M. / Jancarik, J. / Yamaizumi, Z. / Nishimura, S. / Ohtsuka, E. / Kim, S.-H. #3: Journal: Science / Year: 1989 Title: Structure of Ras Protein Authors: Tong, L. / Milburn, M.V. / Devos, A.M. / Kim, S.-H. #4: Journal: Science / Year: 1988 Title: Three-Dimensional Structure of an Oncogene Protein. Catalytic Domain of Human C-H-Ras P21 Authors: Devos, A.M. / Tong, L. / Milburn, M.V. / Matias, P.M. / Jancarik, J. / Noguchi, S. / Nishimura, S. / Miura, K. / Ohtsuka, E. / Kim, S.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q21.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q21.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 4q21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q21_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 4q21_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 4q21_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 4q21_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q21 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q21 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES 60 - 64 ARE DISORDERED. |
-Components
#1: Protein | Mass: 21324.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01112 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.29 % |
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→6 Å / Rfactor Rwork: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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