+Open data
-Basic information
Entry | Database: PDB / ID: 2k3w | ||||||
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Title | NMR structure of VPS4A-MIT-CHMP6 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / ESRCT-III / CHMP6 / MIT / ATP-binding / Membrane / Nucleotide-binding / Transport / Coiled coil / Endosome / Lipoprotein / Myristate | ||||||
Function / homology | Function and homology information vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / ESCRT III complex assembly / 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 / negative regulation of epidermal growth factor-activated receptor activity ...vesicle uncoating / ESCRT complex disassembly / actomyosin contractile ring contraction / ESCRT III complex assembly / 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 / negative regulation of epidermal growth factor-activated receptor activity / late endosome to lysosome transport via multivesicular body sorting pathway / intracellular cholesterol transport / abscission / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / nuclear envelope organization / ESCRT III complex / late endosomal microautophagy / kinetochore microtubule / cytoskeleton-dependent cytokinesis / late endosome to vacuole transport via multivesicular body sorting pathway / mitotic nuclear membrane reassembly / ATP-dependent protein disaggregase activity / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / protein targeting to lysosome / multivesicular body sorting pathway / vesicle budding from membrane / vacuole organization / membrane fission / plasma membrane repair / multivesicular body membrane / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / vesicle-fusing ATPase / Translation of Replicase and Assembly of the Replication Transcription Complex / Flemming body / vacuolar membrane / endosomal transport / mitotic metaphase chromosome alignment / Macroautophagy / ATPase complex / nucleus organization / regulation of protein catabolic process / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / viral release from host cell / regulation of protein localization to plasma membrane / Pyroptosis / nuclear pore / vesicle-mediated transport / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / spindle pole / regulation of protein localization / late endosome / protein transport / late endosome membrane / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / lysosome / early endosome / endosome membrane / endosome / lysosomal membrane / cell division / centrosome / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Kieffer, C. / Skalicky, J.J. / Morita, E. / De Domini, I. / Ward, D.M. / Kaplan, J. / Sundquist, W.I. | ||||||
Citation | Journal: Dev.Cell / Year: 2008 Title: Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 budding Authors: Kieffer, C. / Skalicky, J.J. / Morita, E. / De Domenico, I. / Ward, D.M. / Kaplan, 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 | 2k3w.cif.gz | 538.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k3w.ent.gz | 450.8 KB | Display | PDB format |
PDBx/mmJSON format | 2k3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/2k3w ftp://data.pdbj.org/pub/pdb/validation_reports/k3/2k3w | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9865.304 Da / Num. of mol.: 1 / Fragment: MIT domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4A, VPS4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UN37 |
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#2: Protein/peptide | Mass: 1835.034 Da / Num. of mol.: 1 / Fragment: residues 166-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP6, VPS20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96FZ7 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 75 / pH: 5.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 20 |