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- PDB-2xa0: Crystal structure of BCL-2 in complex with a BAX BH3 peptide -

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Basic information

Entry
Database: PDB / ID: 2xa0
TitleCrystal structure of BCL-2 in complex with a BAX BH3 peptide
Components
  • APOPTOSIS REGULATOR BAX
  • APOPTOSIS REGULATOR BCL-2
KeywordsAPOPTOSIS / CELL DEATH
Function / homology
Function and homology information


Activation, translocation and oligomerization of BAX / Release of apoptotic factors from the mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of developmental process / Pyroptosis / leukocyte homeostasis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex ...Activation, translocation and oligomerization of BAX / Release of apoptotic factors from the mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of developmental process / Pyroptosis / leukocyte homeostasis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / 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 motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / channel inhibitor activity / spermatid differentiation / melanin metabolic process / positive regulation of neuron maturation / myeloid cell apoptotic process / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / cochlear nucleus development / osteoblast proliferation / glycosphingolipid metabolic process / mesenchymal cell development / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell homeostatic proliferation / B cell negative selection / BAK complex / negative regulation of osteoblast proliferation / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / stem cell development / apoptotic process involved in embryonic digit morphogenesis / gland morphogenesis / mitochondrial permeability transition pore complex / sex differentiation / limb morphogenesis / renal system process / mitochondrial fragmentation involved in apoptotic process / apoptotic process involved in blood vessel morphogenesis / regulation of cell-matrix adhesion / post-embryonic camera-type eye morphogenesis / ear development / The NLRP1 inflammasome / dendritic cell apoptotic process / negative regulation of calcium ion transport into cytosol / lymphoid progenitor cell differentiation / establishment or maintenance of transmembrane electrochemical gradient / melanocyte differentiation / T cell apoptotic process / apoptotic process involved in mammary gland involution / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / positive regulation of apoptotic process involved in mammary gland involution / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / regulation of nitrogen utilization / glomerulus development / focal adhesion assembly / negative regulation of T cell apoptotic process / regulation of transmembrane transporter activity / oocyte development / B cell apoptotic process / metanephros development / neuron maturation / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of multicellular organism growth / negative regulation of motor neuron apoptotic process / regulation of viral genome replication / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / positive regulation of epithelial cell apoptotic process / fertilization / response to UV-B / calcium ion transport into cytosol / negative regulation of ossification / response to iron ion / regulation of mitochondrial membrane permeability involved in apoptotic process / mitochondrial fusion / axon regeneration / epithelial cell apoptotic process / negative regulation of mitochondrial depolarization / myeloid cell homeostasis / Bcl-2 family protein complex / motor neuron apoptotic process / positive regulation of smooth muscle cell migration
Similarity search - Function
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 / Blc2-like / Apoptosis Regulator Bcl-x ...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 / 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 Bcl-2 / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKu, B. / Oh, B.H.
CitationJournal: Cell Res. / Year: 2011
Title: Evidence that Inhibition of Bax Activation by Bcl- 2 Involves its Tight and Preferential Interaction with the Bh3 Domain of Bax.
Authors: Ku, B. / Liang, C. / Jung, J.U. / Oh, B.H.
History
DepositionMar 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOPTOSIS REGULATOR BCL-2
B: APOPTOSIS REGULATOR BCL-2
C: APOPTOSIS REGULATOR BAX
D: APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)52,8674
Polymers52,8674
Non-polymers00
Water37821
1
A: APOPTOSIS REGULATOR BCL-2
C: APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)26,4342
Polymers26,4342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-12.1 kcal/mol
Surface area8290 Å2
MethodPISA
2
B: APOPTOSIS REGULATOR BCL-2
D: APOPTOSIS REGULATOR BAX


Theoretical massNumber of molelcules
Total (without water)26,4342
Polymers26,4342
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-14.3 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.973, 81.973, 138.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein APOPTOSIS REGULATOR BCL-2 / BCL-2


Mass: 22861.713 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEX HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)RIG / References: UniProt: P10415
#2: Protein/peptide APOPTOSIS REGULATOR BAX / BAX


Mass: 3572.035 Da / Num. of mol.: 2 / Fragment: BH3 DOMAIN, RESIDUES 52-82 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q07813
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.23 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM ACETATE (PH 4.2), 3.0 M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 14540 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.5 / % possible all: 75.3

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G5M

1g5m


Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
Details: RESIDUES 35-50 OF BCL-2 ARE REPLACED WITH RESIDUES 33-48 OF BCL-XL TO SOLUBILIZE THE PROTEIN AS REPORTED EARLIER (PETROS ET AL, PROC NATL ACAD SCI U S A 98, 3012-3017(2001)) . HOWEVER, THE ...Details: RESIDUES 35-50 OF BCL-2 ARE REPLACED WITH RESIDUES 33-48 OF BCL-XL TO SOLUBILIZE THE PROTEIN AS REPORTED EARLIER (PETROS ET AL, PROC NATL ACAD SCI U S A 98, 3012-3017(2001)) . HOWEVER, THE FINAL MODEL DOES NOT INCLUDE THE ENTIRE BCL- XL SUBSTITUTION REGION, WHOSE ELECTRON DENSITIES WERE NOT OBSERVED.
RfactorNum. reflection% reflection
Rfree0.2422 708 4.6 %
Rwork0.2223 --
obs0.2223 14476 94.1 %
Solvent computationBsol: 44.8143 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.222 Å20 Å20 Å2
2---0.222 Å20 Å2
3---0.443 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 0 21 2733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0092
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.363
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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