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- PDB-5efm: Beclin 1 Flexible-helical Domian (FHD) (141-171) -

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Basic information

Entry
Database: PDB / ID: 5efm
TitleBeclin 1 Flexible-helical Domian (FHD) (141-171)
ComponentsBeclin-1
KeywordsAPOPTOSIS / flexible helix
Function / homology
Function and homology information


cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / 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 ...cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / 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 / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / engulfment of apoptotic cell / suppression by virus of host autophagy / protein targeting to lysosome / early endosome to late endosome transport / late endosome to vacuole transport / cellular response to nitrogen starvation / SMAD protein signal transduction / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / negative regulation of programmed cell death / response to iron(II) ion / phosphatidylinositol-3-phosphate biosynthetic process / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / Macroautophagy / RSV-host interactions / lysosome organization / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / mitophagy / autophagosome maturation / autophagosome assembly / negative regulation of reactive oxygen species metabolic process / neuron development / autophagosome / response to vitamin E / regulation of macroautophagy / amyloid-beta metabolic process / cellular defense response / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / phagocytic vesicle / regulation of cytokinesis / regulation of autophagy / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to lead ion / trans-Golgi network / ISG15 antiviral mechanism / autophagy / cellular response to hydrogen peroxide / GTPase binding / protein-macromolecule adaptor activity / Translation of Replicase and Assembly of the Replication Transcription Complex / protein-containing complex assembly / defense response to virus / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / endosome membrane / response to hypoxia / Ub-specific processing proteases / endosome / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / apoptotic process / ubiquitin protein ligase binding / dendrite / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSinha, S. / Mei, Y.
CitationJournal: Biochemistry / Year: 2016
Title: Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy.
Authors: Mei, Y. / Ramanathan, A. / Glover, K. / Stanley, C. / Sanishvili, R. / Chakravarthy, S. / Yang, Z. / Colbert, C.L. / Sinha, S.C.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7822
Polymers3,6861
Non-polymers961
Water1448
1
A: Beclin-1
hetero molecules

A: Beclin-1
hetero molecules

A: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3466
Polymers11,0583
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area2470 Å2
ΔGint-77 kcal/mol
Surface area3530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.163, 63.163, 63.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

31A-306-

HOH

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Components

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


Mass: 3686.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14457
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.6
Details: 250mM potassium sodium tartrate tetrahydrate, 2.2 M ammonium sulfate, 100mM sodium citrate tribasic dihydrate (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.3776 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 26, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 1.95→44.66 Å / Num. obs: 3490 / % possible obs: 100 % / Redundancy: 75.5 % / Rsym value: 0.16 / Net I/σ(I): 26.3
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 78.1 % / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
Cootmodel building
SHELXDphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→44.66 Å / FOM work R set: 0.6968 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 169 4.84 %
Rwork0.2116 3321 -
obs0.2119 3490 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.28 Å2 / Biso mean: 54.53 Å2 / Biso min: 32.77 Å2
Refinement stepCycle: final / Resolution: 1.95→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms130 0 5 8 143
Biso mean--53.02 54.6 -
Num. residues----15
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009147
X-RAY DIFFRACTIONf_angle_d1.298196
X-RAY DIFFRACTIONf_chiral_restr0.06819
X-RAY DIFFRACTIONf_plane_restr0.00427
X-RAY DIFFRACTIONf_dihedral_angle_d13.69661
LS refinement shellHighest resolution: 1.95 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2164 169 -
Rwork0.2116 3321 -
all-3490 -
obs--100 %

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