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Yorodumi- PDB-1fyr: DIMER FORMATION THROUGH DOMAIN SWAPPING IN THE CRYSTAL STRUCTURE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fyr | ||||||
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Title | DIMER FORMATION THROUGH DOMAIN SWAPPING IN THE CRYSTAL STRUCTURE OF THE GRB2-SH2 AC-PYVNV COMPLEX | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / Grb2 / SH2 domain / phosphopeptide / Met / domain swapping / dimerization / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information : / Signaling by FGFR3 fusions in cancer / : / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / : / hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation ...: / Signaling by FGFR3 fusions in cancer / : / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / : / hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / branching involved in labyrinthine layer morphogenesis / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / STAT5 Activation / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / semaphorin receptor activity / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Interleukin-15 signaling / pancreas development / MET activates PTPN11 / vesicle membrane / MET activates RAP1 and RAC1 / PI3K events in ERBB2 signaling / Costimulation by the CD28 family / Sema4D mediated inhibition of cell attachment and migration / Signaling by LTK / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / Signal regulatory protein family interactions / positive regulation of endothelial cell chemotaxis / negative regulation of Rho protein signal transduction / natural killer cell mediated cytotoxicity / MET activates PTK2 signaling / Regulation of KIT signaling / epidermal growth factor receptor binding / branching morphogenesis of an epithelial tube / positive regulation of actin filament polymerization / GAB1 signalosome / PI-3K cascade:FGFR3 / positive chemotaxis / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / negative regulation of thrombin-activated receptor signaling pathway / PI-3K cascade:FGFR4 / endodermal cell differentiation / PI-3K cascade:FGFR1 / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of MAPK cascade / RHOU GTPase cycle / semaphorin-plexin signaling pathway / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Interleukin-3, Interleukin-5 and GM-CSF signaling / insulin receptor substrate binding / PI3K Cascade / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / EGFR Transactivation by Gastrin / SHC1 events in EGFR signaling / Signalling to RAS / RHO GTPases Activate WASPs and WAVEs / signal transduction in response to DNA damage / fibroblast growth factor receptor signaling pathway / GRB2 events in ERBB2 signaling / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / establishment of skin barrier / Interleukin receptor SHC signaling / Signal attenuation / 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 / phagocytosis / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / basal plasma membrane / SHC-mediated cascade:FGFR1 / MECP2 regulates neuronal receptors and channels / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Schiering, N. / Casale, E. / Caccia, P. / Giordano, P. / Battistini, C. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Dimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex. Authors: Schiering, N. / Casale, E. / Caccia, P. / Giordano, P. / Battistini, C. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Please note it has not been proven that the domain- swapped dimer has biological significance. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fyr.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fyr.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 1fyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fyr_validation.pdf.gz | 398.7 KB | Display | wwPDB validaton report |
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Full document | 1fyr_full_validation.pdf.gz | 402.8 KB | Display | |
Data in XML | 1fyr_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1fyr_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fyr ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyr | HTTPS FTP |
-Related structure data
Related structure data | 1griS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Details | Dimer 1 is formed from chain I and chain J related by NCS (physiological role not demonstrated) / Dimer 2 is formed from chain K and chain L related by NCS (physiological role not demonstrated) |
-Components
#1: Protein | Mass: 13281.041 Da / Num. of mol.: 4 / Fragment: SH2 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P29354, UniProt: P62993*PLUS #2: Protein/peptide | Mass: 599.570 Da / Num. of mol.: 4 / Fragment: RESIDUES 1356-1359 (RESIDUES 0-3 IN COORDINATES) / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence occurs naturally in humans. References: UniProt: P08581 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 11% PEG 3350, 0.5M NaCL, 0.1M MES/NaOH pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 22423 / Num. obs: 22423 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.4→2.58 Å / Rmerge(I) obs: 0.252 / % possible all: 97.7 |
Reflection | *PLUS Num. measured all: 140468 |
Reflection shell | *PLUS % possible obs: 97.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GRI Resolution: 2.4→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: mask / Bsol: 30.84 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNX / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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