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Yorodumi- PDB-3v2x: Crystal Structure of the Peptide Bound Complex of the Ankyrin Rep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v2x | ||||||
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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 / Retinoid metabolism and transport / positive regulation of oligodendrocyte progenitor proliferation / 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 / Retinoid metabolism and transport / positive regulation of oligodendrocyte progenitor proliferation / folate import across plasma membrane / metanephric proximal tubule development / Vitamin D (calciferol) metabolism / ventricular compact myocardium morphogenesis / response to leptin / metal ion transport / protein transporter activity / hormone binding / 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 / coronary vasculature development / insulin-like growth factor I binding / response to vitamin D / transcytosis / protein import / aorta development / cargo receptor activity / negative regulation of BMP signaling pathway / ventricular septum development / positive regulation of neurogenesis / endosomal transport / low-density lipoprotein particle receptor binding / hemoglobin binding / amyloid-beta clearance / positive regulation of endocytosis / brush border / vagina development / endocytic vesicle / response to X-ray / regulation of protein-containing complex assembly / animal organ regeneration / axonal growth cone / response to retinoic acid / clathrin-coated pit / forebrain development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor-mediated endocytosis / kidney development / neural tube closure / endosome lumen / nuclear receptor binding / PDZ domain binding / brush border membrane / sensory perception of sound / cellular response to growth factor stimulus / histone deacetylase binding / SH3 domain binding / endocytosis / male gonad development / protein transport / apical part of cell / regulation of gene expression / heart development / protein-folding chaperone binding / receptor complex / cell population proliferation / endosome / cytoskeleton / apical plasma membrane / response to xenobiotic stimulus / external side of plasma membrane / axon / ubiquitin protein ligase binding / dendrite / calcium ion binding / negative regulation of apoptotic process / protein-containing complex binding / protein kinase binding / cell surface / Golgi apparatus / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 | 3v2x.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v2x.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 3v2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v2x_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 3v2x_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 3v2x_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 3v2x_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/3v2x ftp://data.pdbj.org/pub/pdb/validation_reports/v2/3v2x | HTTPS FTP |
-Related structure data
Related structure data | 3so8SC 3uxgC 3uzdC 3v2oC 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: 18171.551 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: 1192.510 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: 2.02 Å3/Da / Density % sol: 38.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris, pH 6.5, 0.2M NaCl, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 7, 2010 / Details: VariMax HF optics | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 11884 / % possible obs: 92.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Χ2: 1.042 / Net I/σ(I): 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.85→43.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 7.539 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.146 / 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: 59.74 Å2 / Biso mean: 30.7352 Å2 / Biso min: 15.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→43.55 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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