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- PDB-2m03: Solution structure of BCL-xL determined with selective isotope la... -

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Basic information

Entry
Database: PDB / ID: 2m03
TitleSolution structure of BCL-xL determined with selective isotope labelling of I,L,V sidechains
ComponentsBcl-2-like protein 1
KeywordsAPOPTOSIS / BCL-xL / PUMA
Function / homology
Function and homology information


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 dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...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 dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / 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 / NFE2L2 regulating tumorigenic genes / apoptotic mitochondrial changes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of intrinsic apoptotic signaling pathway / germ cell development / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / RAS processing / channel activity / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / spermatogenesis / nuclear membrane / 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 / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol / cytoplasm
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 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...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 / 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
Similarity search - Domain/homology
Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle simulated annealing, molecular dynamics
AuthorsViacava Follis, A. / Royappa, G. / Kriwacki, R.W.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis.
Authors: Follis, A.V. / Chipuk, J.E. / Fisher, J.C. / Yun, M.K. / Grace, C.R. / Nourse, A. / Baran, K. / Ou, L. / Min, L. / White, S.W. / Green, D.R. / Kriwacki, R.W.
History
DepositionOct 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)20,8051
Polymers20,8051
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 20804.918 Da / Num. of mol.: 1 / Mutation: delta(45-84)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2-like 1, BCL2L, BCL2L1, BCLX / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HNCO
1813D HN(CA)CO
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 0.9 mM [U-100% 13C; U-100% 15N; U-95% 2H; Ile,Leu,Val C1H3] BCL-xL, 92% H2O/8% D2O
Solvent system: 92% H2O/8% D2O
SampleConc.: 0.9 mM / Component: BCL-xL-1
Isotopic labeling: [U-100% 13C; U-100% 15N; U-95% 2H; Ile,Leu,Val C1H3]
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: torsion angle simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 524 / NOE intraresidue total count: 40 / NOE long range total count: 109 / NOE medium range total count: 186 / NOE sequential total count: 189 / Hydrogen bond constraints total count: 140 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 115 / Protein psi angle constraints total count: 114
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.57 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 4.66 ° / Maximum upper distance constraint violation: 0.29 Å / Torsion angle constraint violation method: CYANA run output
NMR ensemble rmsDistance rms dev: 0.017 Å / Distance rms dev error: 0.002 Å

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