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Yorodumi- PDB-1sem: STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQ... -
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-Basic information
Entry | Database: PDB / ID: 1sem | ||||||
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Title | STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS | ||||||
Components |
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Keywords | SIGNAL TRANSDUCTION PROTEIN / SRC-HOMOLOGY 3 (SH3) DOMAIN / PEPTIDE-BINDING PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR | ||||||
Function / homology | Function and homology information Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / SHC-mediated cascade:FGFR1 / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 ...Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / SHC-mediated cascade:FGFR1 / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / PI-3K cascade:FGFR4 / RHO GTPases Activate WASPs and WAVEs / Insulin receptor signalling cascade / MET activates RAS signaling / MET activates PI3K/AKT signaling / RHOU GTPase cycle / FLT3 Signaling / PIP3 activates AKT signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR downregulation / PI3K events in ERBB2 signaling / EGFR Transactivation by Gastrin / RAF/MAP kinase cascade / Negative regulation of MET activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Cargo recognition for clathrin-mediated endocytosis / regulation of cell projection organization / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / regulation of nematode larval development / Clathrin-mediated endocytosis / regulation of vulval development / male genitalia development / COP9 signalosome / muscle organ development / epidermal growth factor receptor binding / regulation of MAPK cascade / regulation of cell migration / phosphotyrosine residue binding / epidermal growth factor receptor signaling pathway / signal transduction / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Lim, W.A. / Richards, F.M. / Fox, R.O. | ||||||
Citation | Journal: Nature / Year: 1994 Title: Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Authors: Lim, W.A. / Richards, F.M. / Fox, R.O. #1: Journal: Nature / Year: 1993 Title: The Sh2 and SH3 Domains of Mammalian Grb2 Couple the Egf Receptor to the Ras Activator Msos1 Authors: Rozakis-Adcock, M. / Fernley, R. / Wade, J. / Pawson, T. / Bowtell, D. #2: Journal: Nature / Year: 1992 Title: C. Elegans Cell-Signalling Gene Sem-5 Encodes a Protein with Sh2 and SH3 Domains Authors: Clark, S.G. / Stern, M.J. / Horvitz, H.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sem.cif.gz | 36 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sem.ent.gz | 27.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/1sem ftp://data.pdbj.org/pub/pdb/validation_reports/se/1sem | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6799.510 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: GRB2 / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: P29355 #2: Protein/peptide | Mass: 1100.339 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: Water | ChemComp-HOH / | Source details | MOLECULE_NAME: MSOS, 10-RESIDUE PEPTIDE (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG). PEPTIDE IS FROM ...MOLECULE_NAME: MSOS, 10-RESIDUE PEPTIDE (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG). PEPTIDE IS FROM BIOLOGICAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.46 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 24, 1994 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 6912 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.08 |
Reflection | *PLUS Highest resolution: 2 Å / Rmerge(I) obs: 0.08 |
-Processing
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Refinement | Resolution: 2→7 Å / σ(F): 2 Details: SSBOND CRYSTALS GROWN IN THE PRESENCE OF DTT; DISULFIDE BOND THOUGHT TO FORM AFTER INITIAL EXPOSURE TO X-RAYS; CAUSED STABLE SHIFT IN UNIT CELL DIMENSIONS.
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Refinement step | Cycle: LAST / Resolution: 2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |