+Open data
-Basic information
Entry | Database: PDB / ID: 1yxr | ||||||
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Title | NMR Structure of VPS4A MIT Domain | ||||||
Components | vacuolar protein sorting factor 4A | ||||||
Keywords | PROTEIN TRAFFICKING / VPS4 / MIT domain | ||||||
Function / homology | Function and homology information vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / endosomal vesicle fusion / mitotic cytokinesis checkpoint signaling / positive regulation of viral budding via host ESCRT complex / negative regulation of cytokinesis / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / late endosomal microautophagy / late endosome to lysosome transport via multivesicular body sorting pathway ...vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / endosomal vesicle fusion / mitotic cytokinesis checkpoint signaling / positive regulation of viral budding via host ESCRT complex / negative regulation of cytokinesis / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / late endosomal microautophagy / late endosome to lysosome transport via multivesicular body sorting pathway / abscission / intracellular cholesterol transport / ESCRT III complex disassembly / nuclear envelope organization / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / ATP-dependent protein disaggregase activity / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body sorting pathway / vacuole organization / protein targeting to lysosome / vesicle budding from membrane / plasma membrane repair / membrane fission / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / vesicle-fusing ATPase / vacuolar membrane / endosomal transport / mitotic metaphase chromosome alignment / nucleus organization / ATPase complex / viral budding via host ESCRT complex / autophagosome maturation / viral release from host cell / regulation of protein localization to plasma membrane / nuclear pore / vesicle-mediated transport / Endosomal Sorting Complex Required For Transport (ESCRT) / HCMV Late Events / viral budding from plasma membrane / macroautophagy / Budding and maturation of HIV virion / spindle pole / autophagy / regulation of protein localization / late endosome / late endosome membrane / midbody / endosome / endosome membrane / early endosome / lysosome / cell division / centrosome / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / automated NOE assignment using CYANA, torsion angle dynamics for structure calculations | ||||||
Authors | Scott, J.A. / Gaspar, J. / Stuchell, M. / Alam, S. / Skalicky, J. / Sundquist, W.I. | ||||||
Citation | Journal: To be Published Title: NMR Structure of VPS4A MIT Domain Authors: Scott, J.A. / Gaspar, J. / Stuchell, M. / Alam, S. / Skalicky, J. / Sundquist, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yxr.cif.gz | 538.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yxr.ent.gz | 459 KB | Display | PDB format |
PDBx/mmJSON format | 1yxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yxr_validation.pdf.gz | 347.4 KB | Display | wwPDB validaton report |
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Full document | 1yxr_full_validation.pdf.gz | 469.4 KB | Display | |
Data in XML | 1yxr_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 1yxr_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/1yxr ftp://data.pdbj.org/pub/pdb/validation_reports/yx/1yxr | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9056.336 Da / Num. of mol.: 1 / Fragment: MIT Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: pET16b reengineered to contain a TEV cleavage site in place of the normal factor Xa site Gene: 27183 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UN37 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 3D heteronuclear techniques |
-Sample preparation
Details | Contents: Uniform labeling with 15N and 13C. / Solvent system: 50 mM NaCl, 20 mM sodium phosphate, 10% D2O |
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Sample conditions | Ionic strength: 50 mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: automated NOE assignment using CYANA, torsion angle dynamics for structure calculations Software ordinal: 1 Details: The structures are based on 1432 NOE derived distance constraints, 150 dihedral angle constraints (generated by TALOS) and 114 distance constraints from hydrogen bonds | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 20 |