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- PDB-1g5j: COMPLEX OF BCL-XL WITH PEPTIDE FROM BAD -

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Entry
Database: PDB / ID: 1g5j
TitleCOMPLEX OF BCL-XL WITH PEPTIDE FROM BAD
Components
  • APOPTOSIS REGULATOR BCL-X
  • BAD PROTEIN
KeywordsAPOPTOSIS / complex
Function / homology
Function and homology information


ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / BAD-BCL-2 complex / pore complex assembly / glucose catabolic process / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death ...ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / BAD-BCL-2 complex / pore complex assembly / glucose catabolic process / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / cysteine-type endopeptidase activator activity / 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 / type B pancreatic cell proliferation / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / cellular response to lipid / regulation of growth / AKT phosphorylates targets in the cytosol / positive regulation of mitochondrial membrane potential / Bcl-2 family protein complex / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of T cell differentiation / NFE2L2 regulating tumorigenic genes / positive regulation of B cell differentiation / NRAGE signals death through JNK / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of reproductive process / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of developmental process / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / germ cell development / BH3 domain binding / positive regulation of proteolysis / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors / Activation of BAD and translocation to mitochondria / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of protein localization to plasma membrane / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / ovarian follicle development / extrinsic apoptotic signaling pathway / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / regulation of mitochondrial membrane potential / positive regulation of autophagy / negative regulation of autophagy / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of cytokinesis / epithelial cell proliferation / positive regulation of epithelial cell proliferation / cellular response to amino acid stimulus / cellular response to mechanical stimulus / cellular response to gamma radiation / phospholipid binding / positive regulation of insulin secretion / RAS processing / cellular response to nicotine / male gonad development / endocytosis / cytokine-mediated signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle membrane / glucose homeostasis / channel activity / neuron apoptotic process / spermatogenesis / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / cellular response to hypoxia / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / lipid binding / apoptotic process / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum
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
Bcl-2-like protein 1 / Bcl2-associated agonist of cell death
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsPetros, A.M. / Nettesheim, D.G. / Wang, Y. / Olejniczak, E.T. / Meadows, R.P. / Mack, J. / Swift, K. / Matayoshi, E.D. / Zhang, H. / Thompson, C.B. / Fesik, S.W.
CitationJournal: Protein Sci. / Year: 2000
Title: Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies.
Authors: Petros, A.M. / Nettesheim, D.G. / Wang, Y. / Olejniczak, E.T. / Meadows, R.P. / Mack, J. / Swift, K. / Matayoshi, E.D. / Zhang, H. / Thompson, C.B. / Fesik, S.W.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: APOPTOSIS REGULATOR BCL-X
B: BAD PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0862
Polymers23,0862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein APOPTOSIS REGULATOR BCL-X


Mass: 19976.037 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCLX / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817
#2: Protein/peptide BAD PROTEIN


Mass: 3109.521 Da / Num. of mol.: 1 / Fragment: RESIDUES 140-164 / Mutation: E320K, G321D, G325K / Source method: obtained synthetically / Details: The BAD peptide was chemically synthesized. / References: UniProt: Q92934

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY

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Sample preparation

DetailsContents: 15N-Bcl-xL/unlabeled Bad peptide; 15N,13C-Bcl-xL/unlabelled Bad peptide
Solvent system: H2O; D2O
Sample conditionsIonic strength: 40 mM sodium phosphate / pH: 7 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: Brunger, A. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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