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Yorodumi- PDB-7npb: Crystal structure of 14-3-3 sigma in complex with 20mer Amot-p130... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7npb | |||||||||
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Title | Crystal structure of 14-3-3 sigma in complex with 20mer Amot-p130 peptide and fragment 09 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / protein-peptide complex fragment soaking | |||||||||
Function / homology | Function and homology information establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / positive regulation of embryonic development / Regulation of CDH11 function / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / hippo signaling / gastrulation with mouth forming second / negative regulation of vascular permeability ...establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / positive regulation of embryonic development / Regulation of CDH11 function / blood vessel endothelial cell migration / establishment of epithelial cell polarity / angiostatin binding / hippo signaling / gastrulation with mouth forming second / negative regulation of vascular permeability / Signaling by Hippo / cell-cell junction assembly / regulation of small GTPase mediated signal transduction / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / positive regulation of cell size / keratinocyte proliferation / endocytic vesicle / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / bicellular tight junction / negative regulation of keratinocyte proliferation / positive regulation of blood vessel endothelial cell migration / vasculogenesis / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / stress fiber / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / regulation of cell migration / ruffle / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / negative regulation of angiogenesis / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / intrinsic apoptotic signaling pathway in response to DNA damage / chemotaxis / cell junction / lamellipodium / signaling receptor activity / cytoplasmic vesicle / actin cytoskeleton organization / positive regulation of cell growth / angiogenesis / in utero embryonic development / regulation of cell cycle / cadherin binding / external side of plasma membrane / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | |||||||||
Authors | Centorrino, F. / Ottmann, C. | |||||||||
Funding support | European Union, 1items
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Citation | Journal: Curr Res Struct Biol / Year: 2022 Title: Fragment-based exploration of the 14-3-3/Amot-p130 interface. Authors: Centorrino, F. / Andlovic, B. / Cossar, P. / Brunsveld, L. / Ottmann, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7npb.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7npb.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 7npb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7npb_validation.pdf.gz | 762.6 KB | Display | wwPDB validaton report |
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Full document | 7npb_full_validation.pdf.gz | 763.3 KB | Display | |
Data in XML | 7npb_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 7npb_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/7npb ftp://data.pdbj.org/pub/pdb/validation_reports/np/7npb | HTTPS FTP |
-Related structure data
Related structure data | 7nmaC 7nmwC 7nmxC 7nn2C 7nndC 7nneC 7np2C 7npgC 4jc3S S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 28226.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31947 |
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#2: Protein/peptide | Mass: 2242.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q4VCS5 |
-Non-polymers , 4 types, 412 molecules
#3: Chemical | ChemComp-K7N / | ||||
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.095 M Hepes pH 7.5, 26% PEG 400, 0.19 M CaCl2 and 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→41.75 Å / Num. obs: 60725 / % possible obs: 99.58 % / Redundancy: 13.3 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0991 / Net I/σ(I): 36.29 |
Reflection shell | Resolution: 1.37→1.419 Å / Rmerge(I) obs: 0.5968 / Mean I/σ(I) obs: 3.47 / Num. unique obs: 5935 / CC1/2: 0.938 / % possible all: 97.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JC3 Resolution: 1.37→41.75 Å / SU ML: 0.1187 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.5636 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→41.75 Å
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Refine LS restraints |
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LS refinement shell |
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