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- PDB-6tqr: The crystal structure of the MSP domain of human VAP-A in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tqr | |||||||||||||||
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Title | The crystal structure of the MSP domain of human VAP-A in complex with the Phospho-FFAT motif of STARD3. | |||||||||||||||
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![]() | PROTEIN BINDING / Membrane contact sites / FFAT motif / MSP domain / Endoplasmic reticulum | |||||||||||||||
Function / homology | ![]() vesicle tethering to endoplasmic reticulum / progesterone biosynthetic process / endoplasmic reticulum-endosome membrane contact site / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / organelle membrane contact site / sphingomyelin biosynthetic process / sterol transport / ceramide transport / COPII-coated vesicle budding ...vesicle tethering to endoplasmic reticulum / progesterone biosynthetic process / endoplasmic reticulum-endosome membrane contact site / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / organelle membrane contact site / sphingomyelin biosynthetic process / sterol transport / ceramide transport / COPII-coated vesicle budding / negative regulation by host of viral genome replication / positive regulation by host of viral genome replication / protein localization to endoplasmic reticulum / Sphingolipid de novo biosynthesis / Pregnenolone biosynthesis / phospholipid transport / cholesterol transfer activity / cholesterol transport / azurophil granule membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial transport / cholesterol binding / steroid metabolic process / viral release from host cell / bicellular tight junction / endoplasmic reticulum to Golgi vesicle-mediated transport / cholesterol metabolic process / lipid metabolic process / neuron projection development / microtubule cytoskeleton / late endosome membrane / microtubule binding / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / vesicle / membrane fusion / endosome / cadherin binding / protein heterodimerization activity / protein domain specific binding / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||
![]() | McEwen, A.G. / Poussin-Courmontagne, P. / Di Mattia, T. / Wendling, C. / Cavarelli, J. / Tomasetto, C. / Alpy, F. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. Authors: Di Mattia, T. / Martinet, A. / Ikhlef, S. / McEwen, A.G. / Nomine, Y. / Wendling, C. / Poussin-Courmontagne, P. / Voilquin, L. / Eberling, P. / Ruffenach, F. / Cavarelli, J. / Slee, J. / ...Authors: Di Mattia, T. / Martinet, A. / Ikhlef, S. / McEwen, A.G. / Nomine, Y. / Wendling, C. / Poussin-Courmontagne, P. / Voilquin, L. / Eberling, P. / Ruffenach, F. / Cavarelli, J. / Slee, J. / Levine, T.P. / Drin, G. / Tomasetto, C. / Alpy, F. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.6 KB | Display | ![]() |
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PDB format | ![]() | 187.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.9 KB | Display | ![]() |
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Full document | ![]() | 477.9 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tqsC ![]() 6tqtC ![]() 6tquC ![]() 1z9oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24478.170 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: MSP domain / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1983.762 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phospho-FFAT motif / Source: (synth.) ![]() #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 2000 MME, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→42.26 Å / Num. obs: 42485 / % possible obs: 92.8 % / Redundancy: 3.338 % / Biso Wilson estimate: 38.514 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.133 / Rrim(I) all: 0.248 / Χ2: 1.116 / Net I/σ(I): 4.57 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Z9O Resolution: 1.85→42.26 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 34.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.49 Å2 / Biso mean: 36.8225 Å2 / Biso min: 8.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→42.26 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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