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- PDB-7ofo: NMR structure of the Bak transmembrane helix in lipid nanodiscs -

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Basic information

Entry
Database: PDB / ID: 7ofo
TitleNMR structure of the Bak transmembrane helix in lipid nanodiscs
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / mitochondria / pore formation / Bcl2 proteins
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / BH domain binding / porin activity / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / vagina development / B cell homeostasis / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / animal organ regeneration / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / epithelial cell proliferation / regulation of mitochondrial membrane potential / apoptotic signaling pathway / establishment of localization in cell / response to gamma radiation / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / protein-containing complex binding / apoptotic process / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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, 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 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSperl, L.E. / Hagn, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1035, B13 Germany
CitationJournal: Embo J. / Year: 2021
Title: High-resolution analysis of the conformational transition of pro-apoptotic Bak at the lipid membrane.
Authors: Sperl, L.E. / Ruhrnossl, F. / Schiller, A. / Haslbeck, M. / Hagn, F.
History
DepositionMay 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 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:
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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)3,2451
Polymers3,2451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3170 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 3244.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611

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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 1H-15N NOESY
131isotropic13D 1H-15N-NNH-NOESY

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Sample preparation

DetailsType: membrane
Contents: 400 uM [U-13C; U-15N; U-2H] Bak transmembrane helix, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 95% H2O/5% D2O
Details: Bak TMH in lipid nanodiscs / Label: 2H15N-sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMBak transmembrane helix[U-13C; U-15N; U-2H]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1 mMEDTAnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 315 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
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRFAM-SPARKYU of Wisconsin Madisonpeak picking
NMRFAM-SPARKYU of Wisconsin Madisonchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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