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- PDB-5hhe: Human Beclin 1 coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 5hhe
TitleHuman Beclin 1 coiled-coil domain
ComponentsBeclin-1
KeywordsCELL CYCLE / autophagy regulator / coiled-coil domain / anti-parallel dimer
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
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsMei, Y. / Sinha, S.
CitationJournal: Biochemistry / Year: 2016
Title: Identification of BECN1 and ATG14 Coiled-Coil Interface Residues That Are Important for Starvation-Induced Autophagy.
Authors: Mei, Y. / Su, M. / Sanishvili, R. / Chakravarthy, S. / Colbert, C.L. / Sinha, S.C.
History
DepositionJan 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Aug 17, 2016Group: Database references
Revision 1.4Aug 31, 2016Group: Data collection
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Beclin-1
A: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,5732
Polymers22,5732
Non-polymers00
Water4,594255
1
D: Beclin-1

D: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,5732
Polymers22,5732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4940 Å2
ΔGint-51 kcal/mol
Surface area13730 Å2
MethodPISA
2
A: Beclin-1

A: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,5732
Polymers22,5732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area4990 Å2
ΔGint-51 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.200, 71.575, 58.446
Angle α, β, γ (deg.)90.000, 112.550, 90.000
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: 11286.409 Da / Num. of mol.: 2 / Fragment: UNP entries 175-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197 / Plasmid: pET29b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) pLysS / References: UniProt: Q14457
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 39% 2-methyl-2, 4-pentadiol, 9% PEG400 and 100 mM Tris buffer, pH 7.5.
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 7, 2014
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.46→40.15 Å / Num. obs: 38596 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rsym value: 0.082 / Net I/σ(I): 15.91
Reflection shellResolution: 1.46→1.57 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.02 / % possible all: 97.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q8T

3q8t


Resolution: 1.46→40.15 Å / FOM work R set: 0.8251 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 1921 5 %random selection
Rwork0.1715 36508 --
obs0.1733 38429 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.26 Å2 / Biso mean: 32.34 Å2 / Biso min: 14.67 Å2
Refinement stepCycle: final / Resolution: 1.46→40.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 0 255 1829
Biso mean---43.02 -
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071589
X-RAY DIFFRACTIONf_angle_d0.7042122
X-RAY DIFFRACTIONf_chiral_restr0.043229
X-RAY DIFFRACTIONf_plane_restr0.002291
X-RAY DIFFRACTIONf_dihedral_angle_d14.35664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4564-1.49280.3171310.24442476X-RAY DIFFRACTION94
1.4928-1.53310.3081330.20382560X-RAY DIFFRACTION97
1.5331-1.57830.26111380.18692602X-RAY DIFFRACTION100
1.5783-1.62920.21571370.15742621X-RAY DIFFRACTION100
1.6292-1.68740.20361370.14842585X-RAY DIFFRACTION100
1.6874-1.7550.22581370.15122628X-RAY DIFFRACTION100
1.755-1.83490.25951390.1612629X-RAY DIFFRACTION100
1.8349-1.93160.23821380.16352616X-RAY DIFFRACTION100
1.9316-2.05260.21631370.15622608X-RAY DIFFRACTION100
2.0526-2.21110.19981380.14782628X-RAY DIFFRACTION100
2.2111-2.43360.18381400.14632650X-RAY DIFFRACTION100
2.4336-2.78570.22761370.17072618X-RAY DIFFRACTION100
2.7857-3.50930.171390.172634X-RAY DIFFRACTION100
3.5093-40.150.20091400.18762653X-RAY DIFFRACTION99

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