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Yorodumi- PDB-3v2o: Crystal Structure of the Peptide Bound Complex of the Ankyrin Rep... -
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-Basic information
Entry | Database: PDB / ID: 3v2o | ||||||
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Title | Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2 | ||||||
Components |
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Keywords | PROTEIN BINDING / Structural Genomics Consortium / SGC / ANKRA2 / ANK repeat / LRP2/megalin | ||||||
Function / homology | Function and homology information Transport of RCbl within the body / endocytic hemoglobin import into cell / diol metabolic process / chemoattraction of axon / positive regulation of lipoprotein transport / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of oligodendrocyte progenitor proliferation / Retinoid metabolism and transport / folate import across plasma membrane ...Transport of RCbl within the body / endocytic hemoglobin import into cell / diol metabolic process / chemoattraction of axon / positive regulation of lipoprotein transport / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of oligodendrocyte progenitor proliferation / Retinoid metabolism and transport / folate import across plasma membrane / metanephric proximal tubule development / Vitamin D (calciferol) metabolism / metal ion transport / response to leptin / ventricular compact myocardium morphogenesis / protein transporter activity / hormone binding / protein import / vitamin D metabolic process / neuron projection arborization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / coronary artery morphogenesis / negative regulation of endopeptidase activity / outflow tract septum morphogenesis / response to vitamin D / insulin-like growth factor I binding / transcytosis / coronary vasculature development / cargo receptor activity / low-density lipoprotein particle receptor binding / aorta development / positive regulation of neurogenesis / ventricular septum development / endosomal transport / hemoglobin binding / positive regulation of endocytosis / amyloid-beta clearance / brush border / vagina development / endocytic vesicle / regulation of protein-containing complex assembly / negative regulation of BMP signaling pathway / response to X-ray / animal organ regeneration / axonal growth cone / response to retinoic acid / forebrain development / clathrin-coated pit / receptor-mediated endocytosis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kidney development / neural tube closure / PDZ domain binding / endosome lumen / nuclear receptor binding / brush border membrane / sensory perception of sound / cellular response to growth factor stimulus / SH3 domain binding / endocytosis / histone deacetylase binding / male gonad development / protein transport / apical part of cell / heart development / protein-folding chaperone binding / regulation of gene expression / cell population proliferation / cytoskeleton / receptor complex / endosome / response to xenobiotic stimulus / apical plasma membrane / axon / external side of plasma membrane / dendrite / ubiquitin protein ligase binding / calcium ion binding / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å | ||||||
Authors | Lam, R. / Xu, C. / Bian, C.B. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Sci.Signal. / Year: 2012 Title: Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock. Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / ...Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / Pawson, T. / Yang, X.J. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v2o.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v2o.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 3v2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/3v2o ftp://data.pdbj.org/pub/pdb/validation_reports/v2/3v2o | HTTPS FTP |
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-Related structure data
Related structure data | 3so8SC 3uxgC 3uzdC 3v2xC 3v30C 3v31C 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
#1: Protein | Mass: 20257.834 Da / Num. of mol.: 1 / Fragment: UNP residues 148-313 (ANK repeats) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRA, ANKRA2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q9H9E1 |
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#2: Protein/peptide | Mass: 2112.515 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in rat LRP2/megalin. Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P98158 |
#3: 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: 1.73 Å3/Da / Density % sol: 28.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes, pH 7.5, 0.2M ammonium acetate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97941 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2010 Details: Rosenbaum-Rock high-resolution double-crystal monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97941 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.89→50 Å / Num. obs: 11646 / % possible obs: 95.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.096 / Χ2: 0.996 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SO8 Resolution: 1.89→40.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.297 / WRfactor Rwork: 0.254 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.297 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 63.24 Å2 / Biso mean: 35.2059 Å2 / Biso min: 18.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→40.71 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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