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

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Basic information

Entry
Database: PDB / ID: 5vax
TitleBcl-2 complex with Beclin 1 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 / 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 / stem cell development / positive regulation of autophagosome assembly / lymphoid progenitor cell differentiation / T cell apoptotic process / negative regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / 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 / positive regulation of multicellular organism growth / metanephros development / Regulation of MITF-M-dependent genes involved in apoptosis / focal adhesion assembly / negative regulation of motor neuron apoptotic process / neuron maturation / regulation of viral genome replication / oocyte development / endoplasmic reticulum calcium ion homeostasis / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / 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 / response to iron(II) ion / epithelial cell apoptotic process / 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 / digestive tract morphogenesis / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / B cell lineage commitment / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Macroautophagy / positive regulation of smooth muscle cell migration / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of cardiac muscle hypertrophy / pore complex / RSV-host interactions / p38MAPK cascade / negative regulation of intrinsic apoptotic signaling pathway / T cell homeostasis
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-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-2 / 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 / Beclin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.2Nov 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: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
E: Beclin-1
B: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
F: Beclin-1
C: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
G: Beclin-1
D: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
H: Beclin-1


Theoretical massNumber of molelcules
Total (without water)89,8838
Polymers89,8838
Non-polymers00
Water1,36976
1
A: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
E: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,4712
Polymers22,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-17 kcal/mol
Surface area8350 Å2
MethodPISA
2
B: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
F: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,4712
Polymers22,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-16 kcal/mol
Surface area8520 Å2
MethodPISA
3
C: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
G: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,4712
Polymers22,4712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-19 kcal/mol
Surface area8230 Å2
MethodPISA
4
D: Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera
H: Beclin-1


Theoretical massNumber of molelcules
Total (without water)22,4712
Polymers22,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-19 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.474, 87.174, 126.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 19545.695 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) / Strain (production host): K-12 / References: UniProt: P10415
#2: Protein/peptide
Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 2925.173 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.: 76 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: bis-tris chloride, pH 4.5, 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: 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→50 Å / Num. obs: 50382 / % possible obs: 99.72 % / Redundancy: 7.2 % / Net I/σ(I): 12.88

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XA0

2xa0


Resolution: 2→48.78 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 2515 5 %
Rwork0.2091 --
obs0.2109 50321 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 0 76 5330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075468
X-RAY DIFFRACTIONf_angle_d0.8337408
X-RAY DIFFRACTIONf_dihedral_angle_d9.2794048
X-RAY DIFFRACTIONf_chiral_restr0.047770
X-RAY DIFFRACTIONf_plane_restr0.005955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9996-2.0380.42421330.40452534X-RAY DIFFRACTION97
2.038-2.07960.5051380.42652620X-RAY DIFFRACTION99
2.0796-2.12480.35741350.3362610X-RAY DIFFRACTION100
2.1248-2.17430.3231380.28022623X-RAY DIFFRACTION100
2.1743-2.22860.33881390.26442643X-RAY DIFFRACTION100
2.2286-2.28890.28941390.26852624X-RAY DIFFRACTION100
2.2889-2.35620.28081380.24262622X-RAY DIFFRACTION100
2.3562-2.43230.2791380.23652635X-RAY DIFFRACTION100
2.4323-2.51920.29591390.2182631X-RAY DIFFRACTION100
2.5192-2.62010.28341400.21992665X-RAY DIFFRACTION100
2.6201-2.73930.26421390.20972647X-RAY DIFFRACTION100
2.7393-2.88370.22941410.20622666X-RAY DIFFRACTION100
2.8837-3.06440.24291390.2032644X-RAY DIFFRACTION100
3.0644-3.30090.25291410.21172672X-RAY DIFFRACTION100
3.3009-3.6330.20741420.18622698X-RAY DIFFRACTION100
3.633-4.15850.21781420.17272695X-RAY DIFFRACTION100
4.1585-5.23830.18241430.16652730X-RAY DIFFRACTION100
5.2383-48.79450.2191510.19592847X-RAY DIFFRACTION100

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