+Open data
-Basic information
Entry | Database: PDB / ID: 2ci8 | ||||||
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Title | sh2 domain of human nck1 adaptor protein - uncomplexed | ||||||
Components | CYTOPLASMIC PROTEIN NCK1Cytoplasm | ||||||
Keywords | TRANSLATION / BINDING SPECIFICITY / HOST-PATHOGEN / INTERACTIONS | ||||||
Function / homology | Function and homology information positive regulation of cap-dependent translational initiation / positive regulation of peptidyl-serine dephosphorylation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of cap-independent translational initiation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity ...positive regulation of cap-dependent translational initiation / positive regulation of peptidyl-serine dephosphorylation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / protein phosphatase type 1 complex / positive regulation of translation in response to endoplasmic reticulum stress / positive regulation of cap-independent translational initiation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / substrate-dependent cell migration, cell extension / cytoskeletal anchor activity / vesicle membrane / signal complex assembly / Activation of RAC1 / DCC mediated attractive signaling / Nephrin family interactions / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / protein kinase inhibitor activity / negative regulation of PERK-mediated unfolded protein response / antiviral innate immune response / RHOU GTPase cycle / Generation of second messenger molecules / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / signaling adaptor activity / negative regulation of peptidyl-serine phosphorylation / regulation of cell migration / negative regulation of insulin receptor signaling pathway / molecular condensate scaffold activity / positive regulation of T cell proliferation / response to endoplasmic reticulum stress / T cell activation / ephrin receptor binding / Downstream signal transduction / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / FCGR3A-mediated phagocytosis / PKR-mediated signaling / positive regulation of neuron projection development / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / signaling receptor complex adaptor activity / protein-macromolecule adaptor activity / Potential therapeutics for SARS / ribosome / cadherin binding / protein domain specific binding / signaling receptor binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Frese, S. / Schubert, W.-D. / Findeis, A.C. / Marquardt, T. / Roske, Y.S. / Stradal, T.E.B. / Heinz, D.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: The Phosphotyrosine Peptide Binding Specificity of Nck1 and Nck2 Src Homology 2 Domains. Authors: Frese, S. / Schubert, W.-D. / Findeis, A.C. / Marquardt, T. / Roske, Y.S. / Stradal, T.E.B. / Heinz, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ci8.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ci8.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ci8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2ci8 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2ci8 | HTTPS FTP |
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-Related structure data
Related structure data | 2ci9C 2ciaC 1jyuS C: citing same article (ref.) 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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Components on special symmetry positions |
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Details | THE DIMER IS A STRAND EXCHANGE DIMER AND MAYNOT HAVE BIOLOGICAL SIGNIFICANCE. |
-Components
#1: Protein | Mass: 11514.019 Da / Num. of mol.: 1 / Fragment: SH2-DOMAIN, RESIDUES 281-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 (AMERSHAM BIOSCIENCES) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P16333 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-1PE / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: METHOD: HANGING-DROP, VAPOR-DIFFUSION AT 4 DEGREES C, PROTEIN: 8 MG/ML PROTEIN IN 20 MM TRIS/HCL, PH 8.0, RESERVOIR: 25% PEG5000 MME, 0.1M MES PH 6.5, 0.2M (NH4)2SO4, 0.1M GUANIDINE HCL. CRYOPROTECTANT: 20% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91977 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 17, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91977 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 11119 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.3 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JYU Resolution: 1.8→30.26 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.556 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30.26 Å
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Refine LS restraints |
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