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- PDB-4yj4: Crystal structure of Bcl-xL in complex with the BIM BH3 domain co... -

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Basic information

Entry
Database: PDB / ID: 4yj4
TitleCrystal structure of Bcl-xL in complex with the BIM BH3 domain containing Ile155-to-Arg and Glu158-to-phosphoserine mutations
Components
  • Bcl-2-like protein 1
  • Bcl-2-like protein 1, BIM BH3 domain
KeywordsAPOPTOSIS / Bcl-xL / BIM / BH3
Function / homology
Function and homology information


The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RAS processing / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway ...The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RAS processing / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / apoptotic process in bone marrow cell / ear development / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / meiosis I / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / tube formation / mammary gland development / positive regulation of T cell apoptotic process / regulation of organ growth / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / myeloid cell homeostasis / NRAGE signals death through JNK / response to cycloheximide / thymocyte apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / FOXO-mediated transcription of cell death genes / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / germ cell development / odontogenesis of dentin-containing tooth / B cell homeostasis / BH3 domain binding / ectopic germ cell programmed cell death / 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 / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / FLT3 Signaling / response to endoplasmic reticulum stress / endomembrane system / response to cytokine / release of cytochrome c from mitochondria / thymus development / regulation of mitochondrial membrane potential / epithelial cell proliferation / post-embryonic development / regulation of cytokinesis / cell-matrix adhesion / kidney development / mitochondrion organization / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / mitochondrial membrane / response to radiation / cellular response to gamma radiation / response to virus / synaptic vesicle membrane / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / microtubule binding / nuclear membrane / regulation of apoptotic process / neuron apoptotic process / spermatogenesis / defense response to virus / negative regulation of neuron apoptotic process / in utero embryonic development / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / apoptotic process / centrosome / negative regulation of apoptotic process / protein kinase binding
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
ACETATE ION / Bcl-2-like protein 11 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsKu, B. / Ha, N.-C. / Oh, B.-H.
CitationJournal: Cell Death Dis / Year: 2015
Title: Conversion of cell-survival activity of Akt into apoptotic death of cancer cells by two mutations on the BIM BH3 domain.
Authors: Kim, J.S. / Ku, B. / Woo, T.G. / Oh, A.Y. / Jung, Y.S. / Soh, Y.M. / Yeom, J.H. / Lee, K. / Park, B.J. / Oh, B.H. / Ha, N.C.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_detector / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Bcl-2-like protein 1, BIM BH3 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1365
Polymers25,0062
Non-polymers1303
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-23 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.926, 72.926, 75.458
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 22265.326 Da / Num. of mol.: 1 / Mutation: M83E, A84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl2l1, Bcl2l, Bclx / Production host: Escherichia coli (E. coli) / References: UniProt: Q64373
#2: Protein/peptide Bcl-2-like protein 1, BIM BH3 domain


Mass: 2740.921 Da / Num. of mol.: 1 / Mutation: I155A, E158S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O43521*PLUS
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.8
Details: 0.1 M sodium acetate (pH 4.8), 3.0 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 14211 / % possible obs: 96.4 % / Redundancy: 6.3 % / Net I/σ(I): 34.5

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.1→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2107 --
Rwork0.1831 --
obs0.1831 13580 97.4 %
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 6 143 1513

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