- PDB-5yr0: Structure of Beclin1-UVRAG coiled coil domain complex -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5yr0
Title
Structure of Beclin1-UVRAG coiled coil domain complex
Components
Beclin-1
UV radiation resistance associated protein
Keywords
ENDOCYTOSIS / autophagy regulator
Function / homology
Function and homology information
lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / Macroautophagy / cellular response to aluminum ion / ISG15 antiviral mechanism / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly ...lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / Macroautophagy / cellular response to aluminum ion / ISG15 antiviral mechanism / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / DNA-dependent protein kinase complex / engulfment of apoptotic cell / positive regulation of autophagosome assembly / receptor catabolic process / negative regulation of autophagosome assembly / protein targeting to lysosome / late endosome to vacuole transport / early endosome to late endosome transport / SMAD protein signal transduction / Ub-specific processing proteases / response to other organism / double-strand break repair via classical nonhomologous end joining / negative regulation of programmed cell death / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / centrosome cycle / cellular response to nitrogen starvation / response to iron(II) ion / SNARE complex assembly / phosphatidylinositol-3-phosphate biosynthetic process / spindle organization / cytoplasmic pattern recognition receptor signaling pathway / mitotic metaphase chromosome alignment / lysosome organization / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / autophagosome membrane / autophagosome maturation / autophagosome assembly / chromosome, centromeric region / mitophagy / response to vitamin E / negative regulation of reactive oxygen species metabolic process / neuron development / amyloid-beta metabolic process / regulation of macroautophagy / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / positive regulation of autophagy / phagocytic vesicle / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / autophagosome / cellular response to amino acid starvation / negative regulation of autophagy / SNARE binding / regulation of cytokinesis / regulation of autophagy / chromosome segregation / macroautophagy / response to lead ion / trans-Golgi network / autophagy / SH3 domain binding / cellular response to hydrogen peroxide / late endosome / GTPase binding / protein-macromolecule adaptor activity / midbody / cytoplasmic vesicle / protein-containing complex assembly / angiogenesis / defense response to virus / early endosome / lysosome / cytoskeleton / response to hypoxia / nuclear body / endosome membrane / endosome / symbiont entry into host cell / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / DNA repair / centrosome / ubiquitin protein ligase binding / dendrite / endoplasmic reticulum membrane / negative regulation of apoptotic process / apoptotic process / protein kinase binding / endoplasmic reticulum Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.8→50 Å / Num. obs: 8323 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.7
Reflection shell
Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 22.6
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0222
refinement
MOSFLM
datareduction
SCALA
datascaling
SHARP
phasing
Refinement
Method to determine structure: SIRAS / Resolution: 1.9→35.18 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.572 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19455
419
5 %
RANDOM
Rwork
0.16943
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obs
0.1707
7908
99.55 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å