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- PDB-6dcn: Bcl-xL complex with Beclin 1 BH3 domain T108pThr -

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Basic information

Entry
Database: PDB / ID: 6dcn
TitleBcl-xL complex with Beclin 1 BH3 domain T108pThr
Components
  • BCL-xl protein
  • Beclin-1
KeywordsAPOPTOSIS / Bcl-2 / autophagy / Beclin 1
Function / homology
Function and homology information


cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / engulfment of apoptotic cell / 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 / negative regulation of lysosome organization ...cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / engulfment of apoptotic cell / 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 / negative regulation of lysosome organization / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of autophagosome assembly / dendritic cell proliferation / negative regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / positive regulation of mononuclear cell proliferation / receptor catabolic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / SMAD protein signal transduction / protein targeting to lysosome / early endosome to late endosome transport / negative regulation of dendritic cell apoptotic process / late endosome to vacuole transport / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / phagophore assembly site / fertilization / Translation of Replicase and Assembly of the Replication Transcription Complex / regulation of growth / regulation of mitochondrial membrane permeability / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / negative regulation of programmed cell death / response to iron(II) ion / Bcl-2 family protein complex / lysosome organization / NFE2L2 regulating tumorigenic genes / mitotic metaphase chromosome alignment / apoptotic mitochondrial changes / cytoplasmic pattern recognition receptor signaling pathway / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / Macroautophagy / hepatocyte apoptotic process / positive regulation of cardiac muscle hypertrophy / RSV-host interactions / negative regulation of release of cytochrome c from mitochondria / p38MAPK cascade / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of intrinsic apoptotic signaling pathway / germ cell development / BH3 domain binding / negative regulation of anoikis / autophagosome assembly / response to vitamin E / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / autophagosome maturation / amyloid-beta metabolic process / regulation of macroautophagy / ectopic germ cell programmed cell death / neuron development / negative regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase binding / cellular defense response / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to glucose starvation / mitophagy / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / phagocytic vesicle / JNK cascade / cellular response to copper ion / positive regulation of autophagy / response to cytokine / cellular response to epidermal growth factor stimulus / negative regulation of autophagy / cellular response to amino acid starvation / autophagosome / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to amino acid stimulus / macroautophagy / trans-Golgi network / response to lead ion / cellular response to gamma radiation / autophagy / ISG15 antiviral mechanism / cellular response to hydrogen peroxide / synaptic vesicle membrane
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: 2.444 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 23, 2018ID: 5VB1
Revision 1.0May 23, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL-xl protein
B: BCL-xl protein
D: Beclin-1
C: Beclin-1


Theoretical massNumber of molelcules
Total (without water)41,2584
Polymers41,2584
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-64 kcal/mol
Surface area15620 Å2
2
A: BCL-xl protein
B: BCL-xl protein
D: Beclin-1
C: Beclin-1

A: BCL-xl protein
B: BCL-xl protein
D: Beclin-1
C: Beclin-1


Theoretical massNumber of molelcules
Total (without water)82,5168
Polymers82,5168
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area19390 Å2
ΔGint-155 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.419, 109.419, 97.127
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-xl protein / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 17703.715 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07817
#2: Protein/peptide Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 2925.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14457
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2M NaCl, 10% glycerol

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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: 2.4438→48.934 Å / Num. obs: 22390 / % possible obs: 99.73 % / Redundancy: 10.8 % / CC1/2: 0.998 / Net I/σ(I): 11.13
Reflection shellResolution: 2.4438→2.5049 Å / Num. unique all: 2143 / CC1/2: 0.533

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSvNov 11, 2017data reduction
XDSvNov 11, 2017data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P1L

2p1l


Resolution: 2.444→48.934 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6
RfactorNum. reflection% reflection
Rfree0.2286 1998 8.93 %
Rwork0.1886 --
obs0.1923 22378 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.444→48.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 0 44 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072677
X-RAY DIFFRACTIONf_angle_d0.7963625
X-RAY DIFFRACTIONf_dihedral_angle_d18.2991555
X-RAY DIFFRACTIONf_chiral_restr0.044391
X-RAY DIFFRACTIONf_plane_restr0.004462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4438-2.50490.35841340.29411374X-RAY DIFFRACTION97
2.5049-2.57260.31791400.26861428X-RAY DIFFRACTION100
2.5726-2.64830.28941390.24171431X-RAY DIFFRACTION100
2.6483-2.73380.26571410.21671424X-RAY DIFFRACTION100
2.7338-2.83150.27281400.21831434X-RAY DIFFRACTION100
2.8315-2.94490.26231420.20671448X-RAY DIFFRACTION100
2.9449-3.07890.29881400.22791426X-RAY DIFFRACTION100
3.0789-3.24120.24591430.21321456X-RAY DIFFRACTION100
3.2412-3.44420.26281420.19611455X-RAY DIFFRACTION100
3.4442-3.710.21411440.18721455X-RAY DIFFRACTION100
3.71-4.08320.20411440.16941472X-RAY DIFFRACTION100
4.0832-4.67360.1661440.14971468X-RAY DIFFRACTION100
4.6736-5.88670.21011470.17211506X-RAY DIFFRACTION100
5.8867-48.94350.21761580.17281603X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.8036 Å / Origin y: 2.555 Å / Origin z: 24.0815 Å
111213212223313233
T0.2548 Å20.0218 Å20.0091 Å2-0.4625 Å20.0387 Å2--0.3409 Å2
L0.5814 °20.3172 °20.3265 °2-2.9838 °20.5972 °2--1.4304 °2
S-0.0782 Å °-0.0114 Å °-0.0158 Å °0.0005 Å °0.0281 Å °-0.2726 Å °-0.0519 Å °0.3274 Å °0.0421 Å °
Refinement TLS groupSelection details: all

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