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- PDB-6ijq: Solution structure of BCL-XL bound to P73-TAD peptide -

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Basic information

Entry
Database: PDB / ID: 6ijq
TitleSolution structure of BCL-XL bound to P73-TAD peptide
Components
  • Bcl-2-like protein 1,Bcl-2-like protein 1
  • Tumor protein p73
KeywordsAPOPTOSIS / complex structure
Function / homology
Function and homology information


positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / 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 / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / 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 / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Bcl-2 family protein complex / : / BH domain binding / Regulation of TP53 Activity through Association with Co-factors / NFE2L2 regulating tumorigenic genes / response to cycloheximide / positive regulation of oligodendrocyte differentiation / cellular response to alkaloid / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / STAT5 activation downstream of FLT3 ITD mutants / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ectopic germ cell programmed cell death / mismatch repair / negative regulation of protein localization to plasma membrane / negative regulation of intrinsic apoptotic signaling pathway / 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 / MDM2/MDM4 family protein binding / regulation of mitotic cell cycle / negative regulation of autophagy / release of cytochrome c from mitochondria / transcription corepressor binding / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / regulation of mitochondrial membrane potential / kidney development / protein tetramerization / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / defense response to virus / neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of MAPK cascade / mitochondrial inner membrane / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / positive regulation of apoptotic process / response to xenobiotic stimulus / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / centrosome / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding
Similarity search - Function
Tumour protein p73, SAM 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 / p53 family signature. ...Tumour protein p73, SAM 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 / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / 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 / SAM domain (Sterile alpha motif) / p53-like transcription factor, DNA-binding / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Tumor protein p73 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYoon, M.-K. / Ha, J.-H. / Lee, M.-S. / Chi, S.-W.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Cytoplasmic pro-apoptotic function of the tumor suppressor p73 is mediated through a modified mode of recognition of the anti-apoptotic regulator Bcl-XL.
Authors: Yoon, M.-K. / Kim, B.-Y. / Lee, J.-Y. / Ha, J.-H. / Kim, S.A. / Lee, D.-H. / Lee, M.-S. / Lee, M.-K. / Choi, J.S. / Cho, J.H. / Kim, J.-H. / Kim, S. / Song, J. / Park, S.G. / Park, B.C. / ...Authors: Yoon, M.-K. / Kim, B.-Y. / Lee, J.-Y. / Ha, J.-H. / Kim, S.A. / Lee, D.-H. / Lee, M.-S. / Lee, M.-K. / Choi, J.S. / Cho, J.H. / Kim, J.-H. / Kim, S. / Song, J. / Park, S.G. / Park, B.C. / Bae, K.-H. / Choi, S.U. / Chi, S.-W.
History
DepositionOct 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Tumor protein p73
B: Bcl-2-like protein 1,Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)22,5972
Polymers22,5972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area11060 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Tumor protein p73 / p53-like transcription factor / p53-related protein


Mass: 1791.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15350
#2: Protein Bcl-2-like protein 1,Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 20804.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This construct is 40 residue-deleted mutant (aa 45-84) with the additional first 4 residues and the last 8 residues from expression vector.,This construct is 40 residue-deleted mutant (aa 45- ...Details: This construct is 40 residue-deleted mutant (aa 45-84) with the additional first 4 residues and the last 8 residues from expression vector.,This construct is 40 residue-deleted mutant (aa 45-84) with the additional first 4 residues and the last 8 residues from expression vector.
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D (H)CCH-TOCSY
151isotropic13D 13C/15N-edited NOESY-HSQC
171isotropic115N/13C-edited, 15N/13C-filtered 3D NOESY
162isotropic12D transferred NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-13C; U-15[U-13C; U-15N]N] Bcl-xL, 2 mM p73 peptide, 90% H2O/10% D2OU-13C, 15N-labeled Bcl-xL in complex with unlabeled p73 peptide13C, 15N-unlabeled90% H2O/10% D2O
solution20.1 mM Bcl-XL, 1 mM p73 peptide, 90% H2O/10% D2Op73 peptide bound to Bcl-xL at a molar ratio of 10:1none90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBcl-xL[U-13C; U-15[U-13C; U-15N]N]1
2 mMp73 peptidenone1
0.1 mMBcl-XLnone2
1 mMp73 peptidenone2
Sample conditionsDetails: 20 mM sodium phosphate, pH 6.5. 150 mM NaCl, 2 mM dithiothreitol (DTT), and 10 % (v/v) D2O
Ionic strength: 150 mM / Label: condition1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
Refinement
MethodSoftware ordinal
simulated annealing1
simulated annealing2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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