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- PDB-2k7w: BAX Activation is Initiated at a Novel Interaction Site -

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Basic information

Entry
Database: PDB / ID: 2k7w
TitleBAX Activation is Initiated at a Novel Interaction Site
Components
  • Apoptosis regulator BAX
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / BAX / BIM / BH3 / BCL-2
Function / homology
Function and homology information


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 / BIM-BCL-xl complex / BIM-BCL-2 complex / positive regulation of motor neuron apoptotic process ...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 / BIM-BCL-xl complex / BIM-BCL-2 complex / positive regulation of motor neuron apoptotic process / regulation of developmental pigmentation / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / NTRK3 as a dependence receptor / Sertoli cell proliferation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / glycosphingolipid metabolic process / B cell homeostatic proliferation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / retinal cell programmed cell death / Activation of BIM and translocation to mitochondria / mitochondrial fragmentation involved in apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / Release of apoptotic factors from the mitochondria / mitochondrial permeability transition pore complex / post-embryonic camera-type eye morphogenesis / ear development / apoptotic process involved in mammary gland involution / establishment or maintenance of transmembrane electrochemical gradient / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / meiosis I / regulation of nitrogen utilization / tube formation / mammary gland development / positive regulation of T cell apoptotic process / regulation of organ growth / endoplasmic reticulum calcium ion homeostasis / fertilization / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / mitochondrial fusion / Bcl-2 family protein complex / motor neuron apoptotic process / cellular response to glucocorticoid stimulus / epithelial cell apoptotic process / myeloid cell homeostasis / execution phase of apoptosis / apoptotic mitochondrial changes / hypothalamus development / NRAGE signals death through JNK / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / thymocyte apoptotic process / positive regulation of calcium ion transport into cytosol / pore complex / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / vagina development / BH3 domain binding / germ cell development / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / B cell homeostasis / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of mitochondrial membrane potential / negative regulation of apoptotic signaling pathway / blood vessel remodeling / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / Pyroptosis / ectopic germ cell programmed cell death / cellular response to unfolded protein / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / supramolecular fiber organization / positive regulation of cell cycle / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway / : / release of sequestered calcium ion into cytosol
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 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 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 / 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
Bcl-2-like protein 11 / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGavathiotis, E. / Suzuki, M. / Davis, M.L. / Pitter, K. / Bird, G.H. / Katz, S.G. / Tu, H.C. / Kim, H. / Cheng, E.H. / Tjandra, N. / Walensky, L.D.
CitationJournal: Nature / Year: 2008
Title: BAX activation is initiated at a novel interaction site.
Authors: Gavathiotis, E. / Suzuki, M. / Davis, M.L. / Pitter, K. / Bird, G.H. / Katz, S.G. / Tu, H.C. / Kim, H. / Cheng, E.H. / Tjandra, N. / Walensky, L.D.
History
DepositionAug 27, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis regulator BAX
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)23,6642
Polymers23,6642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1500structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein Apoptosis regulator BAX


Mass: 21204.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-interacting mediator of cell death


Mass: 2459.711 Da / Num. of mol.: 1 / Fragment: BIM BH3 domain / Source method: obtained synthetically / References: UniProt: O43521

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC
NMR detailsText: BAX-BIM SAHB INTERACTION ANALYSIS, PARAMAGNETIC SPIN-LABELING NMR

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Sample preparation

DetailsContents: 0.1-0.2 mM [U-99% 15N] protein, 0.1-0.2 mM peptide, 90% H2O/10%D20
Solvent system: 90% H2O/10%D20
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein[U-99% 15N]0.1-0.21
mMpeptide0.1-0.21
Sample conditionsIonic strength: 50 / pH: 6 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, B. et al.data analysis
CNSBrunger, A. et al.refinement
NMRPipeDelaglio, F. et al.processing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: STRUCTURES CALCULATED WITH HADDOCK 2.0
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1500 / Conformers submitted total number: 20

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