+Open data
-Basic information
Entry | Database: PDB / ID: 2br9 | ||||||
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Title | 14-3-3 Protein Epsilon (Human) Complexed to Peptide | ||||||
Components |
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Keywords | CELL REGULATOR PROTEIN / 14-3-3 / PHOSPHOSERINE / STRUCTURAL GENOMICS CONSORTIUM / SGC / YWHAE | ||||||
Function / homology | Function and homology information : / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / cytoplasmic sequestering of protein / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling ...: / regulation of heart rate by hormone / regulation of potassium ion transmembrane transporter activity / positive regulation of hippo signaling / membrane repolarization during cardiac muscle cell action potential / cytoplasmic sequestering of protein / negative regulation of toll-like receptor signaling pathway / regulation of membrane repolarization / protein localization to endoplasmic reticulum / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / Signaling by Hippo / negative regulation of calcium ion export across plasma membrane / cytoplasmic pattern recognition receptor signaling pathway / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of heart rate by cardiac conduction / regulation of mitotic cell cycle / protein localization to nucleus / phosphoserine residue binding / calcium channel regulator activity / Regulation of HSF1-mediated heat shock response / Activation of BAD and translocation to mitochondria / HSF1 activation / potassium channel regulator activity / protein targeting / calcium channel inhibitor activity / 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 / signaling adaptor activity / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / regulation of cytosolic calcium ion concentration / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / substantia nigra development / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / hippocampus development / TP53 Regulates Metabolic Genes / phosphoprotein binding / neuron migration / mitochondrial membrane / cerebral cortex development / histone deacetylase binding / Regulation of PLK1 Activity at G2/M Transition / MAPK cascade / protein localization / melanosome / MHC class II protein complex binding / cellular response to heat / protein phosphatase binding / scaffold protein binding / transmembrane transporter binding / intracellular signal transduction / cadherin binding / protein domain specific binding / protein heterodimerization activity / focal adhesion / ubiquitin protein ligase binding / enzyme binding / signal transduction / endoplasmic reticulum / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Yang, X. / Elkins, J.M. / Soundararajan, M. / Fedorov, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Doyle, D.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Structural Basis for Protein-Protein Interactions in the 14-3-3 Protein Family. Authors: Yang, X. / Lee, W.H. / Sobott, F. / Papagrigoriou, E. / Robinson, C.V. / Grossmann, J.G. / Sundstrom, M. / Doyle, D.A. / Elkins, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2br9.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2br9.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 2br9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2br9_validation.pdf.gz | 429.6 KB | Display | wwPDB validaton report |
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Full document | 2br9_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 2br9_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2br9_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/2br9 ftp://data.pdbj.org/pub/pdb/validation_reports/br/2br9 | HTTPS FTP |
-Related structure data
Related structure data | 2bq0C 2btpC 2c23C 2c63C 2c74C 1o9dS 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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Details | THE PROTEIN EXISTS IN PHYSIOGICALLY STATE AS A DIMER, HOWEVER, SINCE IN THIS STRUCTURE THIS IS IN COMPLEX WITH A SHORT PEPTIDE (CHAIN P), THE OVERALL COMPLEX IS DESIGNATED AS A TETRAMER. |
-Components
#1: Protein | Mass: 26791.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: THE MAMMALIAN GENE COLLECTION, I.M.A.G.E. CONSORTIUM CLONE ID 3139004 Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62258 |
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#2: Protein/peptide | Mass: 952.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PHOSPHOSERINE AT RESIDUE P 5 / Source: (synth.) HOMO SAPIENS (human) |
#3: Water | ChemComp-HOH / |
Sequence details | THE UNIPROT CROSS-REFERENCE GIVEN IN THE DBREF RECORDS BELOW CORRESPONDS TO GENBANK ENTRY BC000179. ...THE UNIPROT CROSS-REFERENCE GIVEN IN THE DBREF RECORDS BELOW CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.5 % |
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Crystal grow | pH: 8 Details: 40% MPD, 5% PEG10000, 0.1M CACODYLATE PH6.5. PROTEIN IN 150MM NACL, 50MM TRIS PH8, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.968 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→36.42 Å / Num. obs: 138812 / % possible obs: 99.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.9 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O9D Resolution: 1.75→56.34 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.503 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.119 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→56.34 Å
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