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Cryo-EM structure of the polycystin 2-l1 ion channel.

eLife | 2018

We report the near atomic resolution (3.3 Å) of the human polycystic kidney disease 2-like 1 (polycystin 2-l1) ion channel. Encoded by PKD2L1, polycystin 2-l1 is a calcium and monovalent cation-permeant ion channel in primary cilia and plasma membranes. The related primary cilium-specific polycystin-2 protein, encoded by PKD2, shares a high degree of sequence similarity, yet has distinct permeability characteristics. Here we show that these differences are reflected in the architecture of polycystin 2-l1.

Pubmed ID: 30004384 RIS Download

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This is a list of tools and resources that we have found mentioned in this publication.


Visual Molecular Dynamics (tool)

RRID:SCR_001820

A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

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MolProbity (tool)

RRID:SCR_014226

A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot.

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cisTEM (tool)

RRID:SCR_016502

Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

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Coot (software resource)

RRID:SCR_014222

Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.

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Phenix (software resource)

RRID:SCR_014224

A Python-based software suite for the automated determination of molecular structures using X-ray crystallography and other methods. Phenix includes programs for assessing data quality, experimental phasing, molecular replacement, model building, structure refinement, and validation. It also includes tools for reflection data and creating maps and models. Phenix can also be used for neutron crystallography. Tutorials and examples are available in the documentation tab.

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UCSF Chimera (data processing software)

RRID:SCR_004097

A highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use.

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PyMOL (software resource)

RRID:SCR_000305

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Sf9 (cell line)

RRID:CVCL_0549

Cell line Sf9 is a Spontaneously immortalized cell line with a species of origin Spodoptera frugiperda

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HEK293S GnTI- (cell line)

RRID:CVCL_A785

Cell line HEK293S GnTI- is a Transformed cell line with a species of origin Homo sapiens (Human)

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