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- PDB-6dco: Bcl-xL complex with Beclin 1 BH3 domain T108D -

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Basic information

Entry
Database: PDB / ID: 6dco
TitleBcl-xL complex with Beclin 1 BH3 domain T108D
Components
  • Bcl-2-like protein 1,Bcl-2-like protein 1
  • Beclin-1
KeywordsAPOPTOSIS / Bcl-2 / autophagy / Beclin 1
Function / homology
Function and homology information


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 / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of attachment of mitotic spindle microtubules to kinetochore ...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 / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / apoptotic process in bone marrow cell / The NLRP1 inflammasome / engulfment of apoptotic cell / negative regulation of lysosome organization / positive regulation of mononuclear cell proliferation / SMAD protein signal transduction / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / early endosome to late endosome transport / receptor catabolic process / negative regulation of dendritic cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein targeting to lysosome / fertilization / late endosome to vacuole transport / Dengue virus modulates apoptosis / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of growth / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / regulation of mitochondrial membrane permeability / germ cell development / apoptotic mitochondrial changes / Bcl-2 family protein complex / cellular response to nitrogen starvation / NFE2L2 regulating tumorigenic genes / negative regulation of programmed cell death / phosphatidylinositol-3-phosphate biosynthetic process / hepatocyte apoptotic process / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / response to vitamin E / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / Macroautophagy / p38MAPK cascade / response to iron(II) ion / RSV-host interactions / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / ectopic germ cell programmed cell death / negative regulation of anoikis / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / autophagosome maturation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / epithelial cell proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / JNK cascade / mitotic metaphase chromosome alignment / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / cellular response to glucose starvation / cellular defense response / autophagosome assembly / mitophagy / phosphatidylinositol 3-kinase binding / regulation of macroautophagy / positive regulation of intrinsic apoptotic signaling pathway / phagocytic vesicle / response to cytokine / release of cytochrome c from mitochondria / positive regulation of autophagy / negative regulation of autophagy / regulation of mitochondrial membrane potential / autophagosome / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / cellular response to amino acid stimulus / regulation of autophagy / macroautophagy / regulation of cytokinesis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / trans-Golgi network / male gonad development / circadian rhythm / cellular response to gamma radiation / intrinsic apoptotic signaling pathway in response to DNA damage / response to lead ion / ISG15 antiviral mechanism / cellular response to hydrogen peroxide / autophagy / endocytosis
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 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX ...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 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl-2-like protein 1 / Beclin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsLee, E.F. / Smith, B.J. / Smith, N.A. / Yao, S. / Fairlie, W.D.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1049949 Australia
Australian Research Council (ARC)FT150100212 Australia
CitationJournal: Autophagy / Year: 2019
Title: Structural insights into BCL2 pro-survival protein interactions with the key autophagy regulator BECN1 following phosphorylation by STK4/MST1.
Authors: Lee, E.F. / Smith, N.A. / Soares da Costa, T.P. / Meftahi, N. / Yao, S. / Harris, T.J. / Tran, S. / Pettikiriarachchi, A. / Perugini, M.A. / Keizer, D.W. / Evangelista, M. / Smith, B.J. / Fairlie, W.D.
History
DepositionMay 7, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMay 30, 2018ID: 5VB4
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Bcl-2-like protein 1,Bcl-2-like protein 1
B: Bcl-2-like protein 1,Bcl-2-like protein 1
C: Beclin-1
D: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2327
Polymers41,1264
Non-polymers1063
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-85 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.386, 109.386, 96.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Bcl-2-like protein 1,Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 17703.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: Q07817
#2: Protein/peptide Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 2859.177 Da / Num. of mol.: 2 / Mutation: T108D / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14457
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris pH 7.0, 0.2M MgCl2, 2.5M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.198→48.92 Å / Num. obs: 30476 / % possible obs: 99.56 % / Redundancy: 14.1 % / CC1/2: 0.999 / Net I/σ(I): 20.63
Reflection shellResolution: 2.198→2.277 Å / Num. unique obs: 2914 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P1L

2p1l


Resolution: 2.198→48.919 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1997 6.56 %
Rwork0.2028 --
obs0.2047 30439 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.198→48.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 3 43 2648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072658
X-RAY DIFFRACTIONf_angle_d0.8063596
X-RAY DIFFRACTIONf_dihedral_angle_d22.612928
X-RAY DIFFRACTIONf_chiral_restr0.045389
X-RAY DIFFRACTIONf_plane_restr0.004461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1979-2.25280.34661330.31311894X-RAY DIFFRACTION95
2.2528-2.31370.35491400.28731991X-RAY DIFFRACTION100
2.3137-2.38180.30731390.26611997X-RAY DIFFRACTION100
2.3818-2.45870.29091410.26052002X-RAY DIFFRACTION100
2.4587-2.54660.29681420.25532019X-RAY DIFFRACTION100
2.5466-2.64850.2821410.2431999X-RAY DIFFRACTION100
2.6485-2.7690.23931410.22872028X-RAY DIFFRACTION100
2.769-2.9150.27531420.23732017X-RAY DIFFRACTION100
2.915-3.09760.26441430.23262040X-RAY DIFFRACTION100
3.0976-3.33670.25661420.22362019X-RAY DIFFRACTION100
3.3367-3.67240.24811450.20122053X-RAY DIFFRACTION100
3.6724-4.20360.2131460.16762073X-RAY DIFFRACTION100
4.2036-5.29510.19341460.16052087X-RAY DIFFRACTION100
5.2951-48.9310.18021560.18692223X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.801 Å / Origin y: -14.7867 Å / Origin z: 24.1974 Å
111213212223313233
T0.5049 Å2-0.0008 Å20.0516 Å2-0.296 Å2-0.0238 Å2--0.3956 Å2
L2.4279 °2-0.1924 °20.5648 °2-0.4449 °2-0.4499 °2--1.5931 °2
S0.0069 Å °0.0118 Å °-0.2757 Å °-0.0184 Å °-0.0681 Å °-0.0191 Å °0.3316 Å °0.0634 Å °0.0466 Å °
Refinement TLS groupSelection details: all

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