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Yorodumi- PDB-1lfd: CRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RA... -
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-Basic information
Entry | Database: PDB / ID: 1lfd | ||||||
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Title | CRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RAS-INTERACTING DOMAIN OF RALGDS | ||||||
Components |
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Keywords | COMPLEX (RALGDS/RAS) / COMPLEX (RALGDS-RAS) / RAL / EFFECTOR INTERACTION / COMPLEX (RALGDS-RAS) complex | ||||||
Function / homology | Function and homology information p38MAPK events / GTPase regulator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / RAF/MAP kinase cascade / 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 ...p38MAPK events / GTPase regulator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / RAF/MAP kinase cascade / 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 / small GTPase-mediated signal transduction / 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 / brush border / 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 / guanyl-nucleotide exchange factor activity / 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 Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Huang, L. / Hofer, F. / Martin, G.S. / Kim, S.-H. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Structural basis for the interaction of Ras with RalGDS. Authors: Huang, L. / Hofer, F. / Martin, G.S. / Kim, S.H. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Three-Dimensional Structure of the Ras-Interacting Domain of Ralgds Authors: Huang, L. / Weng, X. / Hofer, F. / Martin, G.S. / Kim, S.H. #2: Journal: Nat.Struct.Biol. / Year: 1997 Title: Erratum. Three-Dimensional Structure of the Ras-Interacting Domain of Ralgds Authors: Huang, L. / Weng, X. / Hofer, F. / Martin, G.S. / Kim, S.H. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Activated Ras Interacts with the Ral Guanine Nucleotide Dissociation Stimulator Authors: Hofer, F. / Fields, S. / Schneider, C. / Martin, G.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lfd.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lfd.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lfd_validation.pdf.gz | 525.2 KB | Display | wwPDB validaton report |
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Full document | 1lfd_full_validation.pdf.gz | 532.5 KB | Display | |
Data in XML | 1lfd_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1lfd_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/1lfd ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lfd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 9989.313 Da / Num. of mol.: 2 / Fragment: RAS-INTERACTING DOMAIN, C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Details: BINDS TO ACTIVE HUMAN RAS / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: HUMAN RAS / Plasmid: PGEX98 MADE FROM PGEX2T Gene (production host): C-TERMINAL DOMAIN OF RAT RALGDSB (RESIDUES 767-864) FUSED TO GST PROTEIN Production host: Escherichia coli (E. coli) / Strain (production host): DH-5ALPHA / References: UniProt: Q03386 #2: Protein | Mass: 19004.438 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-171 / Mutation: E31K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC HUMAN RAS GENE IN THE PLASMID / Gene: HUMAN RAS / Plasmid: PGEX98 MADE FROM PGEX2T / Gene (production host): HUMAN RAS / Production host: Escherichia coli (E. coli) / Strain (production host): DH-5ALPHA / References: UniProt: P01112 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 92 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Date: Sep 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. obs: 30504 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.268 / % possible all: 97.5 |
Reflection | *PLUS Num. measured all: 129387 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LXD, 6Q21 Resolution: 2.1→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NO NCS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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