- 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
Title
Crystal structure of BCL-2 in complex with a BAX BH3 peptide
Components
APOPTOSIS REGULATOR BAX
APOPTOSIS REGULATOR BCL-2
Keywords
APOPTOSIS / CELL DEATH
Function / homology
Function and homology information
outer mitochondrial membrane organization / Activation, translocation and oligomerization of BAX / positive regulation of developmental process / Release of apoptotic factors from the mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / leukocyte homeostasis / Pyroptosis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation ...outer mitochondrial membrane organization / Activation, translocation and oligomerization of BAX / positive regulation of developmental process / Release of apoptotic factors from the mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / leukocyte homeostasis / Pyroptosis / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / inner mitochondrial membrane organization / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of glycoprotein biosynthetic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of B cell apoptotic process / positive regulation of melanocyte differentiation / development of secondary sexual characteristics / myeloid cell apoptotic process / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / osteoblast proliferation / cochlear nucleus development / B cell homeostatic proliferation / mesenchymal cell development / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / positive regulation of neuron maturation / BH domain binding / negative regulation of osteoblast proliferation / apoptotic process involved in blood vessel morphogenesis / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / sex differentiation / limb morphogenesis / gland morphogenesis / apoptotic process involved in embryonic digit morphogenesis / renal system process / mitochondrial permeability transition pore complex / regulation of cell-matrix adhesion / T cell apoptotic process / post-embryonic camera-type eye morphogenesis / stem cell development / negative regulation of calcium ion transport into cytosol / melanocyte differentiation / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / lymphoid progenitor cell differentiation / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of dendritic cell apoptotic process / oocyte development / positive regulation of multicellular organism growth / metanephros development / neuron maturation / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / negative regulation of ossification / negative regulation of B cell apoptotic process / response to UV-B / regulation of mitochondrial membrane permeability / response to iron ion / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / cellular respiration / channel activity / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / regulation of mitochondrial membrane permeability involved in apoptotic process / mitochondrial fusion / Bcl-2 family protein complex 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
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.
Rfactor
Num. reflection
% reflection
Rfree
0.2422
708
4.6 %
Rwork
0.2223
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obs
0.2223
14476
94.1 %
Solvent computation
Bsol: 44.8143 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-0.222 Å2
0 Å2
0 Å2
2-
-
-0.222 Å2
0 Å2
3-
-
-
0.443 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2712
0
0
21
2733
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.0092
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.363
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
X-RAY DIFFRACTION
c_mcangle_it
X-RAY DIFFRACTION
c_scbond_it
X-RAY DIFFRACTION
c_scangle_it
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