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- PDB-1bxl: STRUCTURE OF BCL-XL/BAK PEPTIDE COMPLEX, NMR, MINIMIZED AVERAGE S... -

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Basic information

Entry
Database: PDB / ID: 1bxl
TitleSTRUCTURE OF BCL-XL/BAK PEPTIDE COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE
Components
  • BAK PEPTIDE
  • BCL-XL
KeywordsCOMPLEX (APOPTOSIS/PEPTIDE) / APOPTOSIS / ALTERNATIVE SPLICING / COMPLEX (APOPTOSIS-PEPTIDE) / COMPLEX (APOPTOSIS-PEPTIDE) complex
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / apoptotic process in bone marrow cell / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / apoptotic process in bone marrow cell / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / establishment or maintenance of transmembrane electrochemical gradient / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / calcium ion transport into cytosol / fibroblast apoptotic process / response to UV-C / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / porin activity / thymocyte apoptotic process / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / pore complex / cellular response to alkaloid / positive regulation of IRE1-mediated unfolded protein response / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / germ cell development / negative regulation of reproductive process / negative regulation of developmental process / vagina development / B cell homeostasis / BH3 domain binding / positive regulation of calcium ion transport into cytosol / negative regulation of anoikis / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein localization to plasma membrane / ectopic germ cell programmed cell death / 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 / heat shock protein binding / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / intrinsic apoptotic signaling pathway / negative regulation of autophagy / release of cytochrome c from mitochondria / epithelial cell proliferation / regulation of cytokinesis / response to gamma radiation / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / apoptotic signaling pathway / response to hydrogen peroxide / positive regulation of protein-containing complex assembly / establishment of localization in cell / cellular response to mechanical stimulus / cellular response to gamma radiation / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / RAS processing / cellular response to UV / synaptic vesicle membrane / protein-folding chaperone binding / channel activity / neuron apoptotic process / response to ethanol / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / nuclear membrane / defense response to virus
Similarity search - Function
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-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
Bcl-2-like protein 1 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsSattler, M. / Liang, H. / Nettesheim, D. / Meadows, R.P. / Harlan, J.E. / Eberstadt, M. / Yoon, H. / Shuker, S.B. / Chang, B.S. / Minn, A.J. ...Sattler, M. / Liang, H. / Nettesheim, D. / Meadows, R.P. / Harlan, J.E. / Eberstadt, M. / Yoon, H. / Shuker, S.B. / Chang, B.S. / Minn, A.J. / Thompson, C.B. / Fesik, S.W.
CitationJournal: Science / Year: 1997
Title: Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis.
Authors: Sattler, M. / Liang, H. / Nettesheim, D. / Meadows, R.P. / Harlan, J.E. / Eberstadt, M. / Yoon, H.S. / Shuker, S.B. / Chang, B.S. / Minn, A.J. / Thompson, C.B. / Fesik, S.W.
History
DepositionOct 16, 1996Processing site: BNL
Revision 1.0Oct 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 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: BCL-XL
B: BAK PEPTIDE


Theoretical massNumber of molelcules
Total (without water)26,6062
Polymers26,6062
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)1 / -
Representative

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Components

#1: Protein BCL-XL


Mass: 24879.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HMS174 (DE3) / Plasmid: PET29B
Gene (production host): HUMAN BCL-XL, RESIDUES 1-44, 85-205, DELETION MUTANT LACKING A FLEXIBLE LOOP (RESIDUES 45-84) AND THE C-TERMINAL HYDROPHOBIC REGION, WITH A C-TERMINAL HIS-TAG
Production host: Escherichia coli (E. coli) / References: UniProt: Q07817
#2: Protein/peptide BAK PEPTIDE


Mass: 1726.934 Da / Num. of mol.: 1 / Fragment: RESIDUES 572 - 587 OF BAK PROTEIN
Source method: isolated from a genetically manipulated source
References: UniProt: Q16611

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NMR SPECTRA WERE RECORDED ON 1-3 MM SOLUTIONS OF BCL-XL COMPLEXED WITH A BAK PEPTIDE IN 10 MM SODIUM PHOSPHATE BUFFER (PH 6.5) AT 303K.

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Sample preparation

Sample conditionsTemperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 1

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