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- PDB-2bzw: The crystal structure of BCL-XL in complex with full-length BAD -

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Basic information

Entry
Database: PDB / ID: 2bzw
TitleThe crystal structure of BCL-XL in complex with full-length BAD
Components
  • APOPTOSIS REGULATOR BCL-X
  • BCL2-ANTAGONIST OF CELL DEATH
KeywordsTRANSCRIPTION / APOPTOSIS / PHOSPHORYLATION / TRANSCRIPTION COMPLEX / MITOCHONDRION / TRANSMEMBRANE
Function / homology
Function and homology information


positive regulation of granulosa cell apoptotic process / ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / Activation of BAD and translocation to mitochondria / The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / NRAGE signals death through JNK / BAD-BCL-2 complex ...positive regulation of granulosa cell apoptotic process / ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / Activation of BAD and translocation to mitochondria / The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / NRAGE signals death through JNK / BAD-BCL-2 complex / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / protein kinase B binding / BH domain binding / glucose catabolic process / apoptotic process in bone marrow cell / pore complex assembly / symbiont-mediated suppression of host apoptosis / positive regulation of synaptic vesicle endocytosis / cysteine-type endopeptidase activator activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / protein phosphatase 2B binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / type B pancreatic cell proliferation / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / cellular response to lipid / Bcl-2 family protein complex / positive regulation of mitochondrial membrane potential / positive regulation of B cell differentiation / positive regulation of T cell differentiation / response to cycloheximide / clathrin binding / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / hepatocyte apoptotic process / negative regulation of intrinsic apoptotic signaling pathway / germ cell development / positive regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / positive regulation of ATP biosynthetic process / negative regulation of anoikis / BH3 domain binding / extrinsic apoptotic signaling pathway via death domain receptors / regulation of synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / ATP metabolic process / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / regulation of long-term synaptic depression / 14-3-3 protein binding / clathrin-coated pit / response to cytokine / MDM2/MDM4 family protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / response to ischemia / positive regulation of epithelial cell proliferation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of cytokinesis / symbiont-mediated activation of host apoptosis / regulation of mitochondrial membrane potential / mitochondrion organization / cellular response to amino acid stimulus / apoptotic signaling pathway / cellular response to mechanical stimulus / cellular response to gamma radiation / response to radiation / cellular response to nicotine / phospholipid binding / male gonad development / mitochondrial membrane / intrinsic apoptotic signaling pathway in response to DNA damage / response to virus / cytokine-mediated signaling pathway / positive regulation of insulin secretion / synaptic vesicle / glucose homeostasis / synaptic vesicle membrane / presynapse / channel activity / GTPase binding / neuron apoptotic process / protein phosphatase binding / spermatogenesis / regulation of apoptotic process / nuclear membrane / cellular response to hypoxia / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / cell population proliferation
Similarity search - Function
Bcl2-associated agonist of cell death / Pro-apoptotic Bcl-2 protein, BAD / 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 ...Bcl2-associated agonist of cell death / Pro-apoptotic Bcl-2 protein, BAD / 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
Bcl2-associated agonist of cell death / Bcl-2-like protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsLee, K.-H. / Han, W.-D. / Kim, K.-J. / Oh, B.-H.
CitationJournal: Plos Pathog. / Year: 2008
Title: Structural and Biochemical Bases for the Inhibition of Autophagy and Apoptosis by Viral Bcl-2 of Murine Gamma-Herpesvirus 68.
Authors: Ku, B. / Woo, J. / Liang, C. / Lee, K. / Hong, H. / Xiaofeni, E. / Kim, K. / Jung, J.U. / Oh, B.
History
DepositionAug 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Feb 11, 2015Group: Database references / Source and taxonomy
Revision 1.3Dec 14, 2016Group: Database references / Structure summary
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOPTOSIS REGULATOR BCL-X
B: BCL2-ANTAGONIST OF CELL DEATH


Theoretical massNumber of molelcules
Total (without water)26,9512
Polymers26,9512
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-15.3 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.748, 91.748, 58.545
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein APOPTOSIS REGULATOR BCL-X / BCL-XL / BCL-2-LIKE 1 PROTEIN


Mass: 23732.980 Da / Num. of mol.: 1 / Fragment: BCL-2 HOMOLOGY DOMAIN, RESIDUES 1-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: UTERUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIG / References: UniProt: Q64373
#2: Protein/peptide BCL2-ANTAGONIST OF CELL DEATH / BAD / BCL-2 BINDING COMPONENT 6 / BCL-XL/BCL-2 ASSOCIATED DEATH PROMOTER


Mass: 3217.595 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: UTERUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIG / References: UniProt: Q61337
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREGULATES THE CELL DEATH

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 %

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 14382 / % possible obs: 89.3 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.3→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 574 4.6 %RANDOM
Rwork0.2193 ---
obs0.2193 11244 89.3 %-
Solvent computationBsol: 38.0548 Å2 / ksol: 0.352073 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.56 Å2-3.255 Å20 Å2
2---3.138 Å20 Å2
3---5.698 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 0 37 1426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00677
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_deg1.19534
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
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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