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- PDB-2p1l: Structure of the Bcl-XL:Beclin 1 complex -

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Basic information

Entry
Database: PDB / ID: 2p1l
TitleStructure of the Bcl-XL:Beclin 1 complex
Components
  • Apoptosis regulator Bcl-X
  • Beclin 1
KeywordsAPOPTOSIS / autophagy / beclin / BH3 domain / Bcl
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 / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / apoptotic process in bone marrow cell ...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 / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / apoptotic process in bone marrow cell / engulfment of apoptotic cell / The NLRP1 inflammasome / dendritic cell apoptotic process / positive regulation of autophagosome assembly / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / early endosome to late endosome transport / cytoplasmic side of mitochondrial outer membrane / negative regulation of autophagosome assembly / receptor catabolic process / SMAD protein signal transduction / protein targeting to lysosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / late endosome to vacuole transport / negative regulation of dendritic cell apoptotic process / 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 / regulation of mitochondrial membrane permeability / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / fertilization / regulation of growth / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / negative regulation of programmed cell death / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / lysosome organization / mitotic metaphase chromosome alignment / response to cycloheximide / cytoplasmic pattern recognition receptor signaling pathway / response to vitamin E / STAT5 activation downstream of FLT3 ITD mutants / Macroautophagy / hepatocyte apoptotic process / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / negative regulation of release of cytochrome c from mitochondria / cellular response to alkaloid / p38MAPK cascade / RSV-host interactions / negative regulation of intrinsic apoptotic signaling pathway / apoptotic mitochondrial changes / germ cell development / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / negative regulation of anoikis / autophagosome assembly / amyloid-beta metabolic process / autophagosome maturation / regulation of macroautophagy / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein localization to plasma membrane / neuron development / cellular defense response / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / ovarian follicle development / mitophagy / positive regulation of intrinsic apoptotic signaling pathway / phagocytic vesicle / JNK cascade / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / positive regulation of autophagy / negative regulation of autophagy / autophagosome / cellular response to amino acid starvation / cellular response to epidermal growth factor stimulus / cellular response to copper ion / release of cytochrome c from mitochondria / epithelial cell proliferation / regulation of cytokinesis / regulation of mitochondrial membrane potential / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to amino acid stimulus / macroautophagy / trans-Golgi network / cellular response to gamma radiation / circadian rhythm / response to lead ion / autophagy / ISG15 antiviral mechanism / male gonad development
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 / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
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: 2.5 Å
AuthorsJeffrey, P.D. / Shi, Y. / Oberstein, A.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the Bcl-XL-Beclin 1 peptide complex: Beclin 1 is a novel BH3-only protein
Authors: Oberstein, A. / Jeffrey, P.D. / Shi, Y.
History
DepositionMar 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-X
B: Beclin 1
C: Apoptosis regulator Bcl-X
D: Beclin 1
E: Apoptosis regulator Bcl-X
F: Beclin 1
G: Apoptosis regulator Bcl-X
H: Beclin 1


Theoretical massNumber of molelcules
Total (without water)83,5538
Polymers83,5538
Non-polymers00
Water28816
1
A: Apoptosis regulator Bcl-X
B: Beclin 1


Theoretical massNumber of molelcules
Total (without water)20,8882
Polymers20,8882
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-13 kcal/mol
Surface area9560 Å2
MethodPISA
2
C: Apoptosis regulator Bcl-X
D: Beclin 1


Theoretical massNumber of molelcules
Total (without water)20,8882
Polymers20,8882
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-13 kcal/mol
Surface area9740 Å2
MethodPISA
3
E: Apoptosis regulator Bcl-X
F: Beclin 1


Theoretical massNumber of molelcules
Total (without water)20,8882
Polymers20,8882
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-13 kcal/mol
Surface area9660 Å2
MethodPISA
4
G: Apoptosis regulator Bcl-X
H: Beclin 1


Theoretical massNumber of molelcules
Total (without water)20,8882
Polymers20,8882
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area9580 Å2
MethodPISA
5
A: Apoptosis regulator Bcl-X
B: Beclin 1
C: Apoptosis regulator Bcl-X
D: Beclin 1

A: Apoptosis regulator Bcl-X
B: Beclin 1
C: Apoptosis regulator Bcl-X
D: Beclin 1

E: Apoptosis regulator Bcl-X
F: Beclin 1
G: Apoptosis regulator Bcl-X
H: Beclin 1

E: Apoptosis regulator Bcl-X
F: Beclin 1
G: Apoptosis regulator Bcl-X
H: Beclin 1


Theoretical massNumber of molelcules
Total (without water)167,10616
Polymers167,10616
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-x-1/2,y-1/2,-z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area38600 Å2
ΔGint-258 kcal/mol
Surface area55280 Å2
MethodPISA
6
E: Apoptosis regulator Bcl-X
F: Beclin 1
G: Apoptosis regulator Bcl-X
H: Beclin 1


Theoretical massNumber of molelcules
Total (without water)41,7774
Polymers41,7774
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-55 kcal/mol
Surface area14970 Å2
MethodPISA
7
A: Apoptosis regulator Bcl-X
B: Beclin 1
C: Apoptosis regulator Bcl-X
D: Beclin 1


Theoretical massNumber of molelcules
Total (without water)41,7774
Polymers41,7774
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-52 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.940, 110.590, 100.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsUnique heterodimeric complex is formed between chains A and B, (Bcl-XL and Beclin 1 respectively). A dimer of heterodimers is formed between the A+B and C+D complexes via a domain-swapped helix. There are two of these "dimers of heterodimers" in the asymmetric unit.

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Components

#1: Protein
Apoptosis regulator Bcl-X / Bcl-XL / Bcl-2-like 1 protein


Mass: 17506.504 Da / Num. of mol.: 4 / Fragment: Bcl-XL Delta-loop / Mutation: Loop 27-82 deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pRSF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q07817
#2: Protein/peptide
Beclin 1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 3381.751 Da / Num. of mol.: 4 / Fragment: Beclin 1 / Mutation: BH3 domain (residues 107-135)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q14457
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2006
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 46829 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 54.1 Å2 / Rsym value: 0.071 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 4664 / Rsym value: 0.413 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.73 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1611649.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2107 5.1 %RANDOM
Rwork0.226 ---
obs0.225 41260 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.97 Å2 / ksol: 0.337809 e/Å3
Displacement parametersBiso mean: 60.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.03 Å20 Å20 Å2
2--19.33 Å20 Å2
3----13.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5284 0 0 16 5300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 360 5.3 %
Rwork0.302 6487 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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