+Open data
-Basic information
Entry | Database: PDB / ID: 2jq9 | ||||||
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Title | VPS4A MIT-CHMP1A complex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / CHMP1A / VPS4A MIT / Complex / Four Helix Bundle | ||||||
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 endosome to lysosome transport via multivesicular body sorting pathway / abscission ...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 endosome to lysosome transport via multivesicular body sorting pathway / abscission / amphisome membrane / multivesicular body-lysosome fusion / intracellular cholesterol transport / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / nuclear envelope organization / ESCRT III complex / late endosomal microautophagy / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / regulation of centrosome duplication / 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 / membrane fission / plasma membrane repair / late endosome to vacuole transport / 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 / mitotic chromosome condensation / vesicle-fusing ATPase / Flemming body / vacuolar membrane / microtubule organizing center / endosomal transport / mitotic metaphase chromosome alignment / ATPase complex / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / autophagosome maturation / viral release from host cell / regulation of protein localization to plasma membrane / endomembrane system / nuclear pore / vesicle-mediated transport / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / condensed nuclear chromosome / macroautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / nuclear matrix / spindle pole / metallopeptidase activity / regulation of protein localization / protein transport / late endosome / late endosome membrane / midbody / early endosome / lysosome / endosome membrane / endosome / protein domain specific binding / cell division / lysosomal membrane / negative regulation of gene expression / centrosome / protein-containing complex binding / perinuclear region of cytoplasm / protein homodimerization activity / ATP hydrolysis activity / zinc ion binding / extracellular exosome / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | Binary complex of VPS4A MIT domain (residues 1-84) in complex with the C-terminus of CHMP1A (residues 180-196) | ||||||
Authors | Stuchell-Brereton, M.D. / Skalicky, J.J. / Kieffer, C. / Ghaffarian, S. / Sundquist, W.I. | ||||||
Citation | Journal: Nature / Year: 2007 Title: ESCRT-III recognition by VPS4 ATPases. Authors: Stuchell-Brereton, M.D. / Skalicky, J.J. / Kieffer, C. / Karren, M.A. / Ghaffarian, S. / 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 | 2jq9.cif.gz | 596.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jq9.ent.gz | 505.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jq9_validation.pdf.gz | 356.9 KB | Display | wwPDB validaton report |
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Full document | 2jq9_full_validation.pdf.gz | 601.6 KB | Display | |
Data in XML | 2jq9_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 2jq9_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/2jq9 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/2jq9 | HTTPS FTP |
-Related 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: 9865.304 Da / Num. of mol.: 1 / Fragment: MIT domain, residues 1-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4A, VPS4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UN37 |
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#2: Protein/peptide | Mass: 2016.268 Da / Num. of mol.: 1 / Fragment: sequence database residues 180-196 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCOLN3, CHMP1, CHMP1A, KIAA0047, PRSM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HD42 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Binary complex of VPS4A MIT domain (residues 1-84) in complex with the C-terminus of CHMP1A (residues 180-196) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Half-filtered NOESYs provided the intermolecular NOEs |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50 / pH: 5.65 / 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: simulated annealing / Software ordinal: 1 Details: Refinement using anneal.inp and using summed NOE constraints with max T of 3000 K for simulated annealing. | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1311 / NOE intraresidue total count: 309 / NOE long range total count: 278 / NOE medium range total count: 391 / NOE sequential total count: 333 / Hydrogen bond constraints total count: 59 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 76 / Protein psi angle constraints total count: 76 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.03 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0.1 ° / Maximum upper distance constraint violation: 0.017 Å / Torsion angle constraint violation method: CNS | ||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.004 Å |