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- PDB-3pl7: Crystal structure of Bcl-xL in complex with the BaxBH3 domain -

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Basic information

Entry
Database: PDB / ID: 3pl7
TitleCrystal structure of Bcl-xL in complex with the BaxBH3 domain
Components
  • Apoptosis regulator BAX
  • Bcl-2-like protein 1
KeywordsAPOPTOSIS/APOPTOSIS REGULATOR / Bcl-2 family fold / Regulation of apoptosis / Bax / mitochondria / APOPTOSIS-APOPTOSIS REGULATOR complex
Function / homology
Function and homology information


release of matrix enzymes from mitochondria / BAX complex / B cell receptor apoptotic signaling pathway / Activation, translocation and oligomerization of BAX / B cell apoptotic process / positive regulation of apoptotic DNA fragmentation / NTRK3 as a dependence receptor / BAK complex / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process ...release of matrix enzymes from mitochondria / BAX complex / B cell receptor apoptotic signaling pathway / Activation, translocation and oligomerization of BAX / B cell apoptotic process / positive regulation of apoptotic DNA fragmentation / NTRK3 as a dependence receptor / BAK complex / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process / Release of apoptotic factors from the mitochondria / The NLRP1 inflammasome / Transcriptional regulation by RUNX2 / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / establishment or maintenance of transmembrane electrochemical gradient / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / mitochondrial fusion / regulation of mitochondrial membrane permeability / apoptotic mitochondrial changes / execution phase of apoptosis / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / STAT5 activation downstream of FLT3 ITD mutants / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of IRE1-mediated unfolded protein response / pore complex / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / negative regulation of anoikis / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / cellular response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein binding / negative regulation of protein localization to plasma membrane / extrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / response to cytokine / supramolecular fiber organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / apoptotic signaling pathway / negative regulation of autophagy / regulation of mitochondrial membrane potential / Hsp70 protein binding / regulation of cytokinesis / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to virus / positive regulation of protein-containing complex assembly / response to toxic substance / endocytosis / positive regulation of neuron apoptotic process / RAS processing / synaptic vesicle membrane / nuclear envelope / nuclear membrane / channel activity / Interleukin-4 and Interleukin-13 signaling / defense response to virus / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / protein heterodimerization activity / apoptotic process / centrosome / negative regulation of apoptotic process / lipid binding / protein kinase binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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-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
Apoptosis regulator BAX / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.613 Å
AuthorsCzabotar, P.E. / Colman, P.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Mutation to Bax beyond the BH3 domain disrupts interactions with pro-survival proteins and promotes apoptosis
Authors: Czabotar, P.E. / Lee, E.F. / Thompson, G.V. / Wardak, A.Z. / Fairlie, W.D. / Colman, P.M.
History
DepositionNov 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Bcl-2-like protein 1
C: Apoptosis regulator BAX
B: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)45,4473
Polymers45,4473
Non-polymers00
Water68538
1
A: Bcl-2-like protein 1
C: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)24,6422
Polymers24,6422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-14 kcal/mol
Surface area8720 Å2
MethodPISA
2
B: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)20,8051
Polymers20,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.246, 99.050, 113.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 20804.918 Da / Num. of mol.: 2 / Fragment: Bcl-xL, UNP residues 1-209 / Mutation: deletion of residues 45-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817
#2: Protein/peptide Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 3837.381 Da / Num. of mol.: 1 / Fragment: BH3 domain, UNP residues 48-81 / Source method: obtained synthetically / Details: Synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07812
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 13% Peg 6000, 0.2M CaCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95661 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 10, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95661 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 12250 / Num. obs: 12238 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Biso Wilson estimate: 38.92 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 26.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.6-2.6914.60.5916.111981100
2.69-2.814.70.5056.9611981100
2.8-2.9314.60.3629.1511981100
2.93-3.0814.70.28111.411991100
3.08-3.2814.70.19215.512131100
3.28-3.5314.70.1221.912361100
3.53-3.8814.60.08528.712151100
3.88-4.4514.50.06236.812271100
4.45-5.614.30.547.512411100
5.6-5013.40.042501313199.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YXJ

2yxj


Resolution: 2.613→33.544 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 587 4.81 %Random
Rwork0.1857 ---
obs0.1888 12214 99.33 %-
all-12296 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.391 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 243.03 Å2 / Biso min: 6.92 Å2
Baniso -1Baniso -2Baniso -3
1-5.1489 Å20 Å2-0 Å2
2--4.2409 Å2-0 Å2
3----9.3898 Å2
Refinement stepCycle: LAST / Resolution: 2.613→33.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 0 38 2540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082557
X-RAY DIFFRACTIONf_angle_d1.0213451
X-RAY DIFFRACTIONf_dihedral_angle_d16.496913
X-RAY DIFFRACTIONf_chiral_restr0.068361
X-RAY DIFFRACTIONf_plane_restr0.004446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6131-2.8760.33111430.23142794X-RAY DIFFRACTION97
2.876-3.29180.2961490.19032881X-RAY DIFFRACTION100
3.2918-4.14610.22181450.16742928X-RAY DIFFRACTION100
4.1461-33.54670.22661500.18463024X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9104-0.77760.74840.6732-0.45911.1627-0.1326-0.1407-0.10520.03070.14080.1564-0.0328-0.2933-0.00630.0499-0.0385-0.02760.1029-0.02320.068512.389119.556110.8671
21.2337-0.5833-0.16130.3908-0.18022.1693-0.0710.0558-0.0807-0.07360.0127-0.06810.43630.2870.0610.11370.04040.03370.0474-0.03350.103942.89510.258115.2796
31.636-0.8353-0.21534.96070.40.4723-0.26260.05260.2554-0.02290.3903-0.47470.06620.0715-0.13560.1924-0.02550.01960.214-0.0190.200926.711217.101212.4711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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