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- PDB-5yr0: Structure of Beclin1-UVRAG coiled coil domain complex -

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Basic information

Entry
Database: PDB / ID: 5yr0
TitleStructure of Beclin1-UVRAG coiled coil domain complex
Components
  • Beclin-1
  • UV radiation resistance associated protein
KeywordsENDOCYTOSIS / autophagy regulator
Function / homology
Function and homology information


lytic vacuole / maintenance of Golgi location / regulation of catalytic activity / Macroautophagy / ISG15 antiviral mechanism / cellular response to aluminum ion / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II ...lytic vacuole / maintenance of Golgi location / regulation of catalytic activity / Macroautophagy / ISG15 antiviral mechanism / cellular response to aluminum ion / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / engulfment of apoptotic cell / DNA-dependent protein kinase complex / negative regulation of lysosome organization / positive regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / early endosome to late endosome transport / negative regulation of autophagosome assembly / receptor catabolic process / SMAD protein signal transduction / late endosome to vacuole transport / protein targeting to lysosome / Ub-specific processing proteases / response to other organism / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / double-strand break repair via classical nonhomologous end joining / phagophore assembly site / cellular response to nitrogen starvation / spindle organization / centrosome cycle / phosphatidylinositol-3-phosphate biosynthetic process / negative regulation of programmed cell death / mitotic metaphase chromosome alignment / response to vitamin E / lysosome organization / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / SNARE complex assembly / p38MAPK cascade / cytoplasmic pattern recognition receptor signaling pathway / autophagosome membrane / amyloid-beta metabolic process / protein secretion / chromosome, centromeric region / regulation of macroautophagy / autophagosome maturation / neuron development / autophagosome assembly / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / JNK cascade / phagocytic vesicle / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of autophagy / autophagosome / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / negative regulation of autophagy / regulation of autophagy / regulation of cytokinesis / SNARE binding / macroautophagy / trans-Golgi network / chromosome segregation / circadian rhythm / SH3 domain binding / bone development / response to lead ion / autophagy / cellular response to hydrogen peroxide / late endosome / protein-containing complex assembly / GTPase binding / angiogenesis / cytoplasmic vesicle / midbody / defense response to virus / molecular adaptor activity / cytoskeleton / protein-macromolecule adaptor activity / response to hypoxia / early endosome / lysosome / endosome / endosome membrane / nuclear body / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / DNA repair / apoptotic process / symbiont entry into host cell / ubiquitin protein ligase binding / centrosome / dendrite / endoplasmic reticulum membrane
Similarity search - Function
UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region ...UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Beclin-1 / UV radiation resistance-associated protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å
AuthorsPan, X. / Zhao, Y. / He, Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Targeting the potent Beclin 1-UVRAG coiled-coil interaction with designed peptides enhances autophagy and endolysosomal trafficking.
Authors: Wu, S. / He, Y. / Qiu, X. / Yang, W. / Liu, W. / Li, X. / Li, Y. / Shen, H.M. / Wang, R. / Yue, Z. / Zhao, Y.
History
DepositionNov 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beclin-1
B: UV radiation resistance associated protein


Theoretical massNumber of molelcules
Total (without water)11,5892
Polymers11,5892
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-22 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.112, 45.112, 161.524
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-398-

HOH

21B-399-

HOH

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Components

#1: Protein/peptide Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein


Mass: 5971.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Becn1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: O88597
#2: Protein/peptide UV radiation resistance associated protein


Mass: 5617.569 Da / Num. of mol.: 1 / Mutation: C238S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uvrag, Uvrag1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8K245
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M citric acid pH 3.5, 3.0M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 8323 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.7
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 22.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.19455 419 5 %RANDOM
Rwork0.16943 ---
obs0.1707 7908 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.352 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.9→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 0 164 931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.014844
X-RAY DIFFRACTIONr_bond_other_d0.0010.017815
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6621133
X-RAY DIFFRACTIONr_angle_other_deg1.0261.6391942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8485107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.27824.23759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26915202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.138158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02946
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02118
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3851.85397
X-RAY DIFFRACTIONr_mcbond_other2.361.845396
X-RAY DIFFRACTIONr_mcangle_it3.4572.706499
X-RAY DIFFRACTIONr_mcangle_other3.4542.711500
X-RAY DIFFRACTIONr_scbond_it3.4412.405445
X-RAY DIFFRACTIONr_scbond_other3.4382.418446
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.543.436628
X-RAY DIFFRACTIONr_long_range_B_refined10.32225.7931058
X-RAY DIFFRACTIONr_long_range_B_other9.88924.9141015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 27 -
Rwork0.168 564 -
obs--98.34 %

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