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- PDB-8wls: Bcl-xL in complex with HBx BH3 delta C peptide -

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Basic information

Entry
Database: PDB / ID: 8wls
TitleBcl-xL in complex with HBx BH3 delta C peptide
Components
  • Bcl-2-like protein 1
  • Protein X
KeywordsAPOPTOSIS / Complex / interaction
Function / homology
Function and homology information


: / symbiont-mediated arrest of host cell cycle during G2/M transition / apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / 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 ...: / symbiont-mediated arrest of host cell cycle during G2/M transition / apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / 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 / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / apoptotic mitochondrial changes / germ cell development / host cell mitochondrion / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / 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 / viral genome replication / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / 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 / spermatogenesis / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / defense response to virus / nuclear membrane / mitochondrial inner membrane / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / DNA-templated transcription / host cell nucleus / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Transactivation protein X / Trans-activation protein 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 ...Transactivation protein X / Trans-activation protein 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 / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / 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 / Protein X
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodSOLUTION NMR / molecular dynamics
AuthorsKobayashi, N. / Nagata, T. / Kusunoki, H.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06152 Japan
Japan Society for the Promotion of Science (JSPS)20K06524 Japan
Japan Society for the Promotion of Science (JSPS)23K05664 Japan
Japan Agency for Medical Research and Development (AMED)22ak0101097 Japan
Japan Society for the Promotion of Science (JSPS)22K06574 Japan
CitationJournal: Biochemistry / Year: 2024
Title: Structural Insights into the Interaction between the C-Terminal-Deleted BH3-like Motif Peptide of Hepatitis B Virus X Protein and Bcl-x L.
Authors: Kusunoki, H. / Sakamoto, T. / Kobayashi, N. / Kohno, T. / Wakamatsu, K. / Nagata, T.
History
DepositionOct 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: 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
B: Protein X


Theoretical massNumber of molelcules
Total (without water)20,7282
Polymers20,7282
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #20lowest energy

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Components

#1: Protein Bcl-2-like protein 1 /


Mass: 17897.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817
#2: Protein/peptide Protein X / HBx / Peptide X / pX


Mass: 2830.153 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GSHM is vector-derived residues. The C-terminal Glycine is derived from the glycine-serine linker before Bcl-xL in the HBx-linker-Bcl-xL fusion protein.
Source: (gene. exp.) Hepatitis B virus / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YKJ6

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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
122isotropic12D 1H-15N HSQC
132isotropic12D 1H-13C HSQC
142isotropic13D HNCO
152isotropic13D HNCA
1112isotropic13D HN(CA)CB
1102isotropic13D CBCA(CO)NH
192isotropic13D HBHA(CO)NH
182isotropic13D (H)CC(CO)NH
172isotropic13D (H)CCH-TOCSY
162isotropic13D CCH-TOCSY
1122isotropic13D 1H-13C NOESY
1132isotropic13D 1H-15N NOESY
1142isotropic13D [F1] 13C,15N-filtered 1H-13C-NOESY
2152isotropic13D [F1] 13C,15N-filtered 1H-13C-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-15N] HBx-Bcl-xL fusion, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] HBx-Bcl-xL fusion, 1.2 mM Non Bcl-xL, 0.3 mM [U-13C; U-15N] HBx, 90% H2O/10% D2O13C/15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHBx-Bcl-xL fusion[U-15N]1
0.5 mMHBx-Bcl-xL fusion[U-13C; U-15N]2
1.2 mMBcl-xLNon2
0.3 mMHBx[U-13C; U-15N]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM potassium phosphate, 50 mM NaCl, 1 mM DTT50 mMcondition-16.8 1 atm308 K
220 mM Tris-HCl, 50 mM NaCl, 1 mM DTT50 mMcondition-27 1 atm308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
MagRO-NMRViewNaohiro, Kobayashidata analysis
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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