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- PDB-3q8t: Crystal structure of the coiled coil domain of Beclin 1, an essen... -

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Basic information

Entry
Database: PDB / ID: 3q8t
TitleCrystal structure of the coiled coil domain of Beclin 1, an essential autophagy protein
ComponentsBeclin-1
KeywordsAPOPTOSIS / Autophagy / Atg14L UVRAG
Function / homology
Function and homology information


ISG15 antiviral mechanism / cellular response to aluminum ion / Macroautophagy / 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 / positive regulation of stress granule assembly / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore ...ISG15 antiviral mechanism / cellular response to aluminum ion / Macroautophagy / 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 / positive regulation of stress granule assembly / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Ub-specific processing proteases / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / engulfment of apoptotic cell / negative regulation of autophagosome assembly / positive regulation of autophagosome assembly / receptor catabolic process / late endosome to vacuole transport / early endosome to late endosome transport / SMAD protein signal transduction / response to other organism / phagophore assembly site / negative regulation of programmed cell death / response to iron(II) ion / cellular response to nitrogen starvation / phosphatidylinositol-3-phosphate biosynthetic process / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / lysosome organization / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / autophagosome maturation / autophagosome assembly / mitophagy / negative regulation of reactive oxygen species metabolic process / response to vitamin E / amyloid-beta metabolic process / regulation of macroautophagy / neuron development / phosphatidylinositol 3-kinase binding / positive regulation of autophagy / cellular response to glucose starvation / phagocytic vesicle / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / cellular response to copper ion / cellular response to epidermal growth factor stimulus / cellular response to amino acid starvation / autophagosome / negative regulation of autophagy / response to nutrient levels / regulation of cytokinesis / regulation of autophagy / macroautophagy / response to lead ion / trans-Golgi network / autophagy / cellular response to hydrogen peroxide / GTPase binding / protein-macromolecule adaptor activity / protein-containing complex assembly / cytoplasmic vesicle / defense response to virus / molecular adaptor activity / response to hypoxia / nuclear body / endosome membrane / endosome / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / ubiquitin protein ligase binding / dendrite / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / apoptotic process / endoplasmic reticulum / protein-containing complex / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3110 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3110 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsLi, X. / Zhao, Y.
CitationJournal: Nat Commun / Year: 2012
Title: Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG
Authors: Li, X. / He, L. / Che, K.H. / Funderburk, S.F. / Pan, L. / Pan, N. / Zhang, M. / Yue, Z. / Zhao, Y.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beclin-1
B: Beclin-1


Theoretical massNumber of molelcules
Total (without water)23,0562
Polymers23,0562
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-51 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.780, 38.350, 65.750
Angle α, β, γ (deg.)90.00, 97.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 11527.770 Da / Num. of mol.: 2 / Fragment: Coiled Coil Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Becn1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XJ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 45% MPD, 2% PEG400, 100mM Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 5, 2009
RadiationMonochromator: VARIMAX SYSTEM BY OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→35.92 Å / Num. all: 19438 / Num. obs: 19438 / % possible obs: 99.99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.96 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MLPHAREphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→35.92 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.666 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23631 1062 5.2 %RANDOM
Rwork0.20876 ---
obs0.21024 19438 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.905 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.05 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 0 279 1871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221599
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9962128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6275187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4626.538104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.01115358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8031514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021212
X-RAY DIFFRACTIONr_nbd_refined0.2430.2871
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21130
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.232
X-RAY DIFFRACTIONr_mcbond_it1.2431.5987
X-RAY DIFFRACTIONr_mcangle_it1.73221500
X-RAY DIFFRACTIONr_scbond_it3.5293678
X-RAY DIFFRACTIONr_scangle_it5.4344.5628
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 88 -
Rwork0.207 1384 -
obs--100 %

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