+Open data
-Basic information
Entry | Database: PDB / ID: 5tjb | |||||||||||||||||||||||||||
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Title | I-II linker of TRPML1 channel at pH 4.5 | |||||||||||||||||||||||||||
Components | Mucolipin-1 | |||||||||||||||||||||||||||
Keywords | TRANSPORT PROTEIN / endolysosomal lumen / tetramer / calcium and pH regulation | |||||||||||||||||||||||||||
Function / homology | Function and homology information calcium ion export / positive regulation of lysosome organization / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / phagosome maturation / NAADP-sensitive calcium-release channel activity / iron ion transmembrane transporter activity / iron ion transmembrane transport / transferrin transport / Transferrin endocytosis and recycling / cellular response to pH ...calcium ion export / positive regulation of lysosome organization / intracellularly phosphatidylinositol-3,5-bisphosphate-gated monatomic cation channel activity / phagosome maturation / NAADP-sensitive calcium-release channel activity / iron ion transmembrane transporter activity / iron ion transmembrane transport / transferrin transport / Transferrin endocytosis and recycling / cellular response to pH / monoatomic anion channel activity / ligand-gated calcium channel activity / TRP channels / sodium channel activity / monoatomic cation transport / phagocytic cup / autophagosome maturation / potassium channel activity / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to calcium ion / cell projection / calcium ion transmembrane transport / calcium channel activity / phagocytic vesicle membrane / late endosome / late endosome membrane / protein homotetramerization / adaptive immune response / receptor complex / endosome membrane / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / lipid binding / Golgi apparatus / nucleoplasm / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | |||||||||||||||||||||||||||
Authors | Li, M. / Zhang, W.K. / Benvin, N.M. / Zhou, X. / Su, D. / Li, H. / Wang, S. / Michailidis, I.E. / Tong, L. / Li, X. / Yang, J. | |||||||||||||||||||||||||||
Funding support | United States, China, 8items
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Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: Structural basis of dual Ca/pH regulation of the endolysosomal TRPML1 channel. Authors: Minghui Li / Wei K Zhang / Nicole M Benvin / Xiaoyuan Zhou / Deyuan Su / Huan Li / Shu Wang / Ioannis E Michailidis / Liang Tong / Xueming Li / Jian Yang / Abstract: The activities of organellar ion channels are often regulated by Ca and H, which are present in high concentrations in many organelles. Here we report a structural element critical for dual Ca/pH ...The activities of organellar ion channels are often regulated by Ca and H, which are present in high concentrations in many organelles. Here we report a structural element critical for dual Ca/pH regulation of TRPML1, a Ca-release channel crucial for endolysosomal function. TRPML1 mutations cause mucolipidosis type IV (MLIV), a severe lysosomal storage disorder characterized by neurodegeneration, mental retardation and blindness. We obtained crystal structures of the 213-residue luminal domain of human TRPML1 containing three missense MLIV-causing mutations. This domain forms a tetramer with a highly electronegative central pore formed by a novel luminal pore loop. Cysteine cross-linking and cryo-EM analyses confirmed that this architecture occurs in the full-length channel. Structure-function studies demonstrated that Ca and H interact with the luminal pore and exert physiologically important regulation. The MLIV-causing mutations disrupt the luminal-domain structure and cause TRPML1 mislocalization. Our study reveals the structural underpinnings of TRPML1's regulation, assembly and pathogenesis. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tjb.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tjb.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 5tjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tjb_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 5tjb_full_validation.pdf.gz | 428.2 KB | Display | |
Data in XML | 5tjb_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 5tjb_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/5tjb ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tjb | HTTPS FTP |
-Related structure data
Related structure data | 6669C 6670C 5tjaSC 5tjcC 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: 25195.057 Da / Num. of mol.: 1 / Fragment: UNP residues (84-296) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCOLN1, ML4, MSTP080 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / Variant (production host): Rosetta-gami 2 / References: UniProt: Q9GZU1 |
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#2: 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: 2.24 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 200 mM magnesium sulfate, 5.3% PEG 3350, and 100 mM acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 9374 / % possible obs: 99.3 % / Redundancy: 4.7 % / Rsym value: 0.068 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.8 / % possible all: 98.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TJA Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 53.9992 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.02 Å2 / Biso mean: 42.0072 Å2 / Biso min: 24.07 Å2
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Refinement step | Cycle: final / Resolution: 2.4→20 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: 10
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Xplor file |
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