+Open data
-Basic information
Entry | Database: PDB / ID: 2oev | ||||||
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Title | Crystal structure of ALIX/AIP1 | ||||||
Components | Programmed cell death 6-interacting protein | ||||||
Keywords | PROTEIN TRANSPORT / coiled-coil / tetratricopeptide repeat / TPR | ||||||
Function / homology | Function and homology information proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / viral budding / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of membrane permeability / regulation of centrosome duplication ...proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly / viral budding / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / regulation of membrane permeability / regulation of centrosome duplication / midbody abscission / multivesicular body sorting pathway / bicellular tight junction assembly / actomyosin / positive regulation of exosomal secretion / multivesicular body assembly / Flemming body / RIPK1-mediated regulated necrosis / viral budding via host ESCRT complex / mitotic cytokinesis / Uptake and function of anthrax toxins / immunological synapse / bicellular tight junction / endoplasmic reticulum exit site / macroautophagy / Budding and maturation of HIV virion / protein homooligomerization / Regulation of necroptotic cell death / calcium-dependent protein binding / extracellular vesicle / melanosome / protein transport / endosome / focal adhesion / centrosome / apoptotic process / protein homodimerization activity / extracellular exosome / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Fisher, R.D. / Zhai, Q. / Robinson, H. / Hill, C.P. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: Structural and Biochemical Studies of ALIX/AIP1 and Its Role in Retrovirus Budding Authors: Fisher, R.D. / Chung, H.Y. / Zhai, Q. / Robinson, H. / Sundquist, W.I. / Hill, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oev.cif.gz | 282.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oev.ent.gz | 234.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/2oev ftp://data.pdbj.org/pub/pdb/validation_reports/oe/2oev | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 78974.695 Da / Num. of mol.: 1 / Fragment: Bro1-V Domains, residues 1-698 / Mutation: K268Y, K269Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6IP, AIP1, ALIX, KIAA1375 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+(RIL) / References: UniProt: Q8WUM4 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 8% PEG 4000, 0.1M ammonium acetate, 0.1M magnesium acetate, 0.05M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. all: 16218 / Num. obs: 14236 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 3.3→3.42 Å / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.5 / % possible all: 64.9 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 79.773 / SU ML: 0.605 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.706 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 137.477 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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