+Open data
-Basic information
Entry | Database: PDB / ID: 5j1t | ||||||
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Title | TorsinAdeltaE-LULL1 complex, H. sapiens, bound to VHH-BS2 | ||||||
Components |
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Keywords | HYDROLASE / AAA+ ATPase / Torsin / endoplasmic reticulum | ||||||
Function / homology | Function and homology information synaptic vesicle membrane organization / nuclear membrane organization / organelle organization / regulation of dopamine uptake involved in synaptic transmission / nuclear envelope organization / protein localization to nuclear envelope / intermediate filament cytoskeleton organization / protein deneddylation / regulation of protein localization to cell surface / positive regulation of synaptic vesicle endocytosis ...synaptic vesicle membrane organization / nuclear membrane organization / organelle organization / regulation of dopamine uptake involved in synaptic transmission / nuclear envelope organization / protein localization to nuclear envelope / intermediate filament cytoskeleton organization / protein deneddylation / regulation of protein localization to cell surface / positive regulation of synaptic vesicle endocytosis / misfolded protein binding / membrane organization / endoplasmic reticulum organization / positive regulation of ATP-dependent activity / wound healing, spreading of cells / synaptic vesicle transport / kinesin binding / ATPase activator activity / chaperone cofactor-dependent protein refolding / protein localization to nucleus / ERAD pathway / chaperone-mediated protein folding / cytoskeletal protein binding / secretory granule / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic vesicle membrane / nuclear envelope / Cargo recognition for clathrin-mediated endocytosis / neuron projection development / unfolded protein binding / synaptic vesicle / ATPase binding / nuclear membrane / growth cone / response to oxidative stress / cytoskeleton / cell adhesion / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 Å | ||||||
Authors | Demircioglu, F.E. / Schwartz, T.U. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2016 Title: Structures of TorsinA and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia. Authors: Demircioglu, F.E. / Sosa, B.A. / Ingram, J. / Ploegh, H.L. / Schwartz, T.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j1t.cif.gz | 292.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j1t.ent.gz | 241.4 KB | Display | PDB format |
PDBx/mmJSON format | 5j1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j1t_validation.pdf.gz | 797.1 KB | Display | wwPDB validaton report |
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Full document | 5j1t_full_validation.pdf.gz | 805.1 KB | Display | |
Data in XML | 5j1t_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 5j1t_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/5j1t ftp://data.pdbj.org/pub/pdb/validation_reports/j1/5j1t | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32614.311 Da / Num. of mol.: 1 / Mutation: E171Q, deltaE302/303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOR1A, DQ2, DYT1, TA, TORA / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR References: UniProt: O14656, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#2: Protein | Mass: 26729.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOR1AIP2, IFRG15, LULL1 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: Q8NFQ8 |
-Antibody , 1 types, 1 molecules C
#3: Antibody | Mass: 13296.745 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR |
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-Non-polymers , 5 types, 636 molecules
#4: Chemical | ChemComp-ATP / | ||
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#5: Chemical | ChemComp-MG / | ||
#6: Chemical | ChemComp-CL / | ||
#7: Chemical | #8: 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: 2.42 Å3/Da / Density % sol: 49.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 19 % PEG3350 200 mM ammonium sulfate 100 mM Bis-Tris/HCl pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.402→67.733 Å / Num. obs: 134334 / % possible obs: 97.06 % / Redundancy: 12.4 % / Biso Wilson estimate: 16.72 Å2 / Rsym value: 0.1 / Net I/σ(I): 30.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.402→67.733 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.79 Å2 / Biso mean: 25.3491 Å2 / Biso min: 10.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.402→67.733 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: 16
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