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Yorodumi- PDB-2ci9: Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ci9 | ||||||
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Title | Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir | ||||||
Components |
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Keywords | PROTEIN BINDING / PROTEIN-BINDING / SH2-DOMAIN-COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / positive regulation of peptidyl-serine dephosphorylation / 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 / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension ...positive regulation of cap-dependent translational initiation / negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation / eukaryotic initiation factor eIF2 binding / positive regulation of peptidyl-serine dephosphorylation / 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 / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / vesicle membrane / signal complex assembly / Activation of RAC1 / Nephrin family interactions / DCC mediated attractive signaling / lamellipodium assembly / RHOV GTPase cycle / positive regulation of actin filament polymerization / negative regulation of PERK-mediated unfolded protein response / protein kinase inhibitor activity / 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 / positive regulation of T cell proliferation / regulation of cell migration / T cell activation / negative regulation of insulin receptor signaling pathway / response to endoplasmic reticulum stress / ephrin receptor binding / Downstream signal transduction / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / molecular condensate scaffold activity / actin filament organization / FCGR3A-mediated phagocytosis / PKR-mediated signaling / receptor tyrosine kinase binding / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / cell-cell junction / signaling receptor complex adaptor activity / cell migration / protein-macromolecule adaptor activity / Potential therapeutics for SARS / ribosome / cadherin binding / protein domain specific binding / signaling receptor binding / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ci9.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ci9.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ci9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2ci9 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2ci9 | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 11751.317 Da / Num. of mol.: 2 / 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 #2: Protein/peptide | Mass: 1468.391 Da / Num. of mol.: 2 Fragment: PHOSPHOPEPTIDE LIGAND OF NCK-SH2, RESIDUES 469-480 Source method: obtained synthetically / Details: THE PEPTIDE WAS SYNTHESIZED CHEMICALLY / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: O50190, UniProt: B7UM99*PLUS #3: 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: 2.26 Å3/Da / Density % sol: 45 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: TECHNIQUE: HANGING-DROP, VAPOR-DIFFUSION PROTEIN CONCENTRATION: 8MG/ML PROTEIN:LIGAND = 1:1.1 RESERVOIRE: 2.4M (NH4)2HPO4, 0.1M TRIS, PH 8.5 CRYOCONDITIONS: 50% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004 / Details: 2 AU-COATED X-RAY MIRRORS |
Radiation | Monochromator: ROEMO TYPE DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 38419 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.2 / % possible all: 88 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NCK1-APO Resolution: 1.5→28.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.033 / SU ML: 0.059 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.105 / 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: 11.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→28.02 Å
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