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- PDB-6l95: transmembrane-domain of Bax -

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Basic information

Entry
Database: PDB / ID: 6l95
Titletransmembrane-domain of Bax
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / Bax / transmembrane-domain / dimer / micelle
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / channel activity / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / germ cell development / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / ectopic germ cell programmed cell death / cellular response to unfolded protein / blood vessel remodeling / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / response to gamma radiation / apoptotic signaling pathway / neuron migration / positive regulation of protein-containing complex assembly / response to toxic substance / cerebral cortex development / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process
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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like ...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
Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBo, O.Y. / Fujiao, L.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504804 China
CitationJournal: To Be Published
Title: transmembrane-domain of Bax
Authors: Bo, O.Y. / Fujiao, L.
History
DepositionNov 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 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

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)5,8192
Polymers5,8192
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area870 Å2
ΔGint-14 kcal/mol
Surface area4880 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 2909.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07812

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D TROSY-HSQC
121isotropic1TROSY-HNCA
131isotropic1TROSY-HN(CO)CA
141isotropic1TROSY-HNCO
151isotropic1TROSY-HN(CA)CO
161isotropic1TROSY-HN(CA)CB
171isotropic13D 15N NOE-TROSY-HSQC
182isotropic23D 15N NOE-TROSY-HSQC
192isotropic23D 13C NOE-HSQC
1102isotropic22D 1H-13C HSQC
1113isotropic23D 15N NOE-TROSY-HSQC
1133isotropic22D TROSY-HSQC
1124isotropic32D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.6 mM [U-98% 15N;U-98% 13C;U-98% 2H] human bax helix9, 0.1 % DPC, 25 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O15N_13C_2H_sample90% H2O/10% D2O
micelle20.6 mM [U-98% 15N;U-98% 13C] human bax helix9, 0.1 % [U-2H] DPC, 25 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
micelle30.3 mM [U-98% 15N;U-2H] human bax helix9, 0.1 % [U-2H] DPC, 25 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O15N_2H_sample90% H2O/10% D2O
membrane50.3 mM [U-98% 13C] human bax helix9, 0.1 % [U-2H] DPC, 25 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O13C_sample90% H2O/10% D2O
micelle40.4 mM [U-98% 15N;U-15% 13C] human bax helix9, 0.1 % DPC, 25 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O15N_15%_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMhuman bax helix9[U-98% 15N;U-98% 13C;U-98% 2H]1
0.1 %DPCnatural abundance1
25 mMHEPESnatural abundance1
150 mMsodium chloridenatural abundance1
0.6 mMhuman bax helix9[U-98% 15N;U-98% 13C]2
0.1 %DPC[U-2H]2
25 mMHEPESnatural abundance2
150 mMsodium chloridenatural abundance2
0.3 mMhuman bax helix9[U-98% 15N;U-2H]3
0.1 %DPC[U-2H]3
25 mMHEPESnatural abundance3
150 mMsodium chloridenatural abundance3
0.3 mMhuman bax helix9[U-98% 13C]5
0.1 %DPC[U-2H]5
25 mMHEPESnatural abundance5
150 mMsodium chloridenatural abundance5
0.4 mMhuman bax helix9[U-98% 15N;U-15% 13C]4
0.1 %DPCnatural abundance4
25 mMHEPESnatural abundance4
150 mMsodium chloridenatural abundance4
Sample conditionsIonic strength: 150 mM / Label: con_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002
A DD2ADD28003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
XEASYBartels et al.chemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorepeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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