+Open data
-Basic information
Entry | Database: PDB / ID: 3c3q | ||||||
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Title | ALIX Bro1-domain:CHMIP4B co-crystal structure | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / ALIX CHMP4B BRO1 amphipathic-helix / Cataract / Disease mutation / Protein transport / Transport / Apoptosis / Host-virus interaction | ||||||
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 / maintenance of lens transparency / regulation of extracellular exosome assembly / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / extracellular exosome biogenesis ...proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / maintenance of lens transparency / regulation of extracellular exosome assembly / amphisome membrane / multivesicular body-lysosome fusion / viral budding / vesicle fusion with vacuole / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / regulation of membrane permeability / late endosome to vacuole transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / post-translational protein targeting to endoplasmic reticulum membrane / multivesicular body sorting pathway / vesicle budding from membrane / bicellular tight junction assembly / actomyosin / membrane fission / plasma membrane repair / membrane coat / multivesicular body membrane / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / exit from mitosis / multivesicular body assembly / regulation of mitotic spindle assembly / nervous system process / Translation of Replicase and Assembly of the Replication Transcription Complex / Flemming body / nucleus organization / RIPK1-mediated regulated necrosis / Macroautophagy / mitotic metaphase chromosome alignment / viral budding via host ESCRT complex / autophagosome maturation / autophagosome membrane / mitotic cytokinesis / Uptake and function of anthrax toxins / immunological synapse / protein polymerization / bicellular tight junction / Pyroptosis / endoplasmic reticulum exit site / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / multivesicular body / viral budding from plasma membrane / HCMV Late Events / regulation of autophagy / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / protein homooligomerization / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / kinetochore / autophagy / calcium-dependent protein binding / extracellular vesicle / melanosome / protein transport / nuclear envelope / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / vesicle / endosome / cadherin binding / lysosomal membrane / focal adhesion / centrosome / apoptotic process / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | McCullough, J.B. / Fisher, R.D. / Whitby, F.G. / Sundquist, W.I. / Hill, C.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: ALIX-CHMP4 interactions in the human ESCRT pathway. Authors: McCullough, J. / Fisher, R.D. / Whitby, F.G. / 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 | 3c3q.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c3q.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 3c3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/3c3q ftp://data.pdbj.org/pub/pdb/validation_reports/c3/3c3q | 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: 42735.789 Da / Num. of mol.: 1 / Fragment: BRO1 domain (UNP residues 1-359) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6IP, AIP1, ALIX, KIAA1375 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUM4 |
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#2: Protein/peptide | Mass: 2158.277 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: CHMP4B peptide chemically synthesized. This sequence is found naturally in Homo sapiens (humans). References: UniProt: Q9H444 |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2008 / Details: VARIMAX-HR Confocal Optic |
Radiation | Monochromator: Copper anode, varimax confocal optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 26458 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 67.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→36.64 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.881 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.227 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.926 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→36.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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