+Open data
-Basic information
Entry | Database: PDB / ID: 1nrv | ||||||
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Title | Crystal structure of the SH2 domain of Grb10 | ||||||
Components | Growth factor receptor-bound protein 10 | ||||||
Keywords | SIGNALING PROTEIN / DIMER | ||||||
Function / homology | Function and homology information vascular associated smooth muscle cell migration / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of glycogen biosynthetic process / negative regulation of phosphorylation / negative regulation of glucose import / positive regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of Wnt signaling pathway / IRS activation / RET signaling / Signal attenuation ...vascular associated smooth muscle cell migration / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of glycogen biosynthetic process / negative regulation of phosphorylation / negative regulation of glucose import / positive regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of Wnt signaling pathway / IRS activation / RET signaling / Signal attenuation / positive regulation of phosphorylation / negative regulation of insulin receptor signaling pathway / ERK1 and ERK2 cascade / FLT3 Signaling / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / response to insulin / insulin receptor binding / Signaling by SCF-KIT / signaling receptor complex adaptor activity / gene expression / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein-containing complex / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Stein, E.G. / Hubbard, S.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structural basis for dimerization of the Grb10 Src homology 2 domain. Implications for ligand specificity. Authors: Stein, E.G. / Ghirlando, R. / Hubbard, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nrv.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nrv.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/1nrv ftp://data.pdbj.org/pub/pdb/validation_reports/nr/1nrv | HTTPS FTP |
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-Related structure data
Related structure data | 1a81S 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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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS THE DIMER IN THE ASYMMETRIC UNIT. |
-Components
#1: Protein | Mass: 12361.202 Da / Num. of mol.: 2 / Fragment: SH2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRB10 OR GRBIR OR KIAA0207 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q13322 #2: 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: 42.76 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: May 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 27261 / Num. obs: 26168 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.84 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.37 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 74325 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A81 Resolution: 1.65→28.63 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.14 Å | |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→28.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.02
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Refinement | *PLUS Lowest resolution: 30.9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.223 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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