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- PDB-5vay: Bcl-2 complex with Beclin 1 T108D BH3 domain -

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Basic information

Entry
Database: PDB / ID: 5vay
TitleBcl-2 complex with Beclin 1 T108D BH3 domain
Components
  • Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
  • Beclin-1
KeywordsAPOPTOSIS / Bcl-2 / autophagy / Beclin 1
Function / homology
Function and homology information


cellular response to aluminum ion / channel inhibitor activity / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / phosphatidylinositol 3-kinase complex, class III ...cellular response to aluminum ion / channel inhibitor activity / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / phosphatidylinositol 3-kinase complex, class III / positive regulation of melanocyte differentiation / melanin metabolic process / cellular response to oxygen-glucose deprivation / engulfment of apoptotic cell / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / myeloid cell apoptotic process / positive regulation of stress granule assembly / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / response to mitochondrial depolarisation / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / gland morphogenesis / apoptotic process in bone marrow cell / renal system process / regulation of cell-matrix adhesion / ear development / The NLRP1 inflammasome / dendritic cell apoptotic process / negative regulation of calcium ion transport into cytosol / SARS-CoV-1-mediated effects on programmed cell death / stem cell development / positive regulation of autophagosome assembly / dendritic cell proliferation / lymphoid progenitor cell differentiation / negative regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / positive regulation of mononuclear cell proliferation / T cell apoptotic process / melanocyte differentiation / receptor catabolic process / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / protein targeting to lysosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / SMAD protein signal transduction / early endosome to late endosome transport / B cell apoptotic process / negative regulation of dendritic cell apoptotic process / late endosome to vacuole transport / regulation of nitrogen utilization / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of multicellular organism growth / metanephros development / Regulation of MITF-M-dependent genes involved in apoptosis / neuron maturation / focal adhesion assembly / negative regulation of motor neuron apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of viral genome replication / oocyte development / endoplasmic reticulum calcium ion homeostasis / 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 / response to UV-B / calcium ion transport into cytosol / phosphatidylinositol-3-phosphate biosynthetic process / response to iron ion / negative regulation of ossification / negative regulation of programmed cell death / cellular response to nitrogen starvation / motor neuron apoptotic process / negative regulation of mitochondrial depolarization / axon regeneration / Bcl-2 family protein complex / epithelial cell apoptotic process / response to iron(II) ion / smooth muscle cell migration / lysosome organization / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / organ growth / negative regulation of B cell apoptotic process / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / apoptotic mitochondrial changes / mitotic metaphase chromosome alignment / digestive tract morphogenesis / cytoplasmic pattern recognition receptor signaling pathway
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-2 / Apoptosis regulator, Bcl-X ...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-2 / 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
Apoptosis regulator Bcl-2 / Bcl-2-like protein 1 / Beclin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsLee, E.F. / Smith, B.J. / Yao, S. / Fairlie, W.D.
CitationJournal: To Be Published
Title: Bcl-2 complex with Beclin 1 pT108 BH3 domain
Authors: Lee, E.F. / Smith, B.J. / Yao, S. / Fairlie, W.D.
History
DepositionMar 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
B: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
C: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
D: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
E: Beclin-1
G: Beclin-1
F: Beclin-1
H: Beclin-1


Theoretical massNumber of molelcules
Total (without water)89,4438
Polymers89,4438
Non-polymers00
Water4,612256
1
A: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
E: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,3612
Polymers22,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-15 kcal/mol
Surface area8510 Å2
MethodPISA
2
B: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
F: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,3612
Polymers22,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-12 kcal/mol
Surface area8810 Å2
MethodPISA
3
C: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
G: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,3612
Polymers22,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-14 kcal/mol
Surface area7900 Å2
MethodPISA
4
D: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
H: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,3612
Polymers22,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-15 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.205, 53.192, 91.413
Angle α, β, γ (deg.)90.00, 108.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19501.686 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2, BCL2L1, BCL2L, BCLX / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P10415, UniProt: Q07817
#2: Protein/peptide
Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 2859.177 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14457
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350

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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: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 71186 / % possible obs: 98.95 % / Redundancy: 3.7 % / Net I/σ(I): 14.41

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XA0

2xa0


Resolution: 1.804→50 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.36
RfactorNum. reflection% reflection
Rfree0.228 3559 5 %
Rwork0.1836 --
obs0.1857 71180 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.804→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 0 256 5548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075659
X-RAY DIFFRACTIONf_angle_d0.9797680
X-RAY DIFFRACTIONf_dihedral_angle_d13.3042030
X-RAY DIFFRACTIONf_chiral_restr0.041792
X-RAY DIFFRACTIONf_plane_restr0.0051008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.804-1.82870.31651370.29482598X-RAY DIFFRACTION95
1.8287-1.85490.29991430.2592712X-RAY DIFFRACTION99
1.8549-1.88260.3131400.24332660X-RAY DIFFRACTION99
1.8826-1.9120.26031410.23642681X-RAY DIFFRACTION99
1.912-1.94330.28211410.22822684X-RAY DIFFRACTION99
1.9433-1.97680.27691440.21682724X-RAY DIFFRACTION99
1.9768-2.01280.26861390.21052653X-RAY DIFFRACTION99
2.0128-2.05150.22611420.21072704X-RAY DIFFRACTION99
2.0515-2.09340.28181420.20932685X-RAY DIFFRACTION99
2.0934-2.13890.24021420.20672704X-RAY DIFFRACTION99
2.1389-2.18860.24441420.19432705X-RAY DIFFRACTION99
2.1886-2.24340.23781420.19012685X-RAY DIFFRACTION99
2.2434-2.3040.27241420.18652706X-RAY DIFFRACTION99
2.304-2.37180.25121410.18822671X-RAY DIFFRACTION99
2.3718-2.44840.25611440.18782731X-RAY DIFFRACTION99
2.4484-2.53590.2121410.18412697X-RAY DIFFRACTION99
2.5359-2.63740.21521430.19092713X-RAY DIFFRACTION99
2.6374-2.75740.25581430.18192705X-RAY DIFFRACTION99
2.7574-2.90270.19581420.17922707X-RAY DIFFRACTION99
2.9027-3.08460.1951430.19052720X-RAY DIFFRACTION99
3.0846-3.32270.2591450.18152754X-RAY DIFFRACTION99
3.3227-3.65690.21121420.16152696X-RAY DIFFRACTION99
3.6569-4.18570.18921440.15842739X-RAY DIFFRACTION99
4.1857-5.27220.1871470.14632784X-RAY DIFFRACTION100
5.2722-44.4510.22721470.18362803X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 78.0455 Å / Origin y: 8.1132 Å / Origin z: 22.4968 Å
111213212223313233
T0.201 Å2-0.0042 Å20.0183 Å2-0.1578 Å20.0064 Å2--0.2179 Å2
L0.3118 °20.044 °20.1203 °2-0.0349 °20.0919 °2--0.2898 °2
S-0.0179 Å °0.0878 Å °0.0053 Å °-0.0121 Å °0.0007 Å °-0.0118 Å °-0.0065 Å °0.0215 Å °0.0154 Å °
Refinement TLS groupSelection details: all

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