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- PDB-6l8v: membrane-bound Bax helix2-helix5 domain -

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Basic information

Entry
Database: PDB / ID: 6l8v
Titlemembrane-bound Bax helix2-helix5 domain
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / Bax / membrane-bound / stability / core-domain / dimer
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / 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 / BAX complex / protein insertion into mitochondrial membrane / 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 / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / glycosphingolipid metabolic process / B cell homeostatic proliferation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / mitochondrial fragmentation involved in apoptotic process / apoptotic process involved in blood vessel morphogenesis / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / 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 / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / B cell apoptotic process / regulation of nitrogen utilization / endoplasmic reticulum calcium ion homeostasis / positive regulation of epithelial cell apoptotic process / fertilization / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / epithelial cell apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / execution phase of apoptosis / apoptotic mitochondrial changes / hypothalamus development / thymocyte apoptotic process / positive regulation of calcium ion transport into cytosol / pore complex / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / odontogenesis of dentin-containing tooth / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / BH3 domain binding / B cell homeostasis / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of mitochondrial membrane potential / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / blood vessel remodeling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / Pyroptosis / cellular response to unfolded protein / ectopic germ cell programmed cell death / negative regulation of fibroblast proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / supramolecular fiber organization / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway / homeostasis of number of cells within a tissue / release of sequestered calcium ion into cytosol / response to salt stress / negative regulation of protein binding / Hsp70 protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / regulation of mitochondrial membrane potential / kidney development / response to gamma radiation / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / cerebral cortex development / cellular response to virus / response to toxic substance / intrinsic apoptotic signaling pathway in response to DNA damage / neuron migration / cellular response to UV / positive regulation of neuron apoptotic process / nuclear envelope / channel activity / retina development in camera-type eye / regulation of 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-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
Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsOuYang, B. / Lv, F.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504804 China
CitationJournal: Embo J. / Year: 2021
Title: An amphipathic Bax core dimer forms part of the apoptotic pore wall in the mitochondrial membrane.
Authors: Lv, F. / Qi, F. / Zhang, Z. / Wen, M. / Kale, J. / Piai, A. / Du, L. / Wang, S. / Zhou, L. / Yang, Y. / Wu, B. / Liu, Z. / Del Rosario, J. / Pogmore, J. / Chou, J.J. / Andrews, D.W. / Lin, J. / OuYang, B.
History
DepositionNov 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 / _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 1.3May 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: Apoptosis regulator BAX
B: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)17,9812
Polymers17,9812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2840 Å2
ΔGint-24 kcal/mol
Surface area12240 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 Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 8990.265 Da / Num. of mol.: 2 / Mutation: C62S, C126S
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-HN(CA)CO
151isotropic1TROSY-HNCO
1151isotropic1TROSY-HN(CA)CB
161isotropic13D 15N NOE-TROSY-HSQC
172isotropic23D 15N NOE-TROSY-HSQC
182isotropic23D 13C NOE-HSQC
192isotropic22D 1H-13C HSQC
1103isotropic23D 15N NOE-TROSY-HSQC
1113isotropic22D TROSY-HSQC
1124isotropic23D 15N NOE-TROSY-HSQC
1134isotropic22D TROSY-HSQC
1145isotropic32D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
bicelle10.5 mM U-98% 15N;U-98% 13C;U-98% 2H human Bax core domain, 100 mM DMPC, 140 mM DHPC, 10 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O15N_13C_2H_sample90% H2O/10% D2O
bicelle20.6 mM U-98% 15N;U-98% 13C Bax a_2_a_5, 100 mM [U-2H] DMPC, 160 mM [U-2H] DHPC, 10 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
bicelle30.4 mM U-98% 15N;U-2H Bax a_2_a_5, 120 mM [U-2H] DMPC, 200 mM [U-2H] DHPC, 10 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O15N_2H_sample90% H2O/10% D2O
bicelle60.4 mM U-98% 13C Bax a_2_a_5, 120 mM [U-2H] DMPC, 200 mM [U-2H] DHPC, 10 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O13C_sample90% H2O/10% D2O
bicelle40.6 mM U-98% 15N;U-2H Bax a_2_a_5, 100 mM DMPC, 160 mM [U-2H] DHPC, 10 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O15N_2H_sample90% H2O/10% D2OThe sample was prepared for lipid NOE.
bicelle50.4 mM U-98% 15N;U-15% 13C Bax a_2_a_5, 80 mM DMPC, 140 mM DHPC, 10 mM MES, 100 mM sodium chloride, 90% H2O/10% D2O15N_15%_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMhuman Bax core domainU-98% 15N;U-98% 13C;U-98% 2H1
100 mMDMPCnatural abundance1
140 mMDHPCnatural abundance1
10 mMMESnatural abundance1
100 mMsodium chloridenatural abundance1
0.6 mMBax a_2_a_5U-98% 15N;U-98% 13C2
100 mMDMPC[U-2H]2
160 mMDHPC[U-2H]2
10 mMMESnatural abundance2
100 mMsodium chloridenatural abundance2
0.4 mMBax a_2_a_5U-98% 15N;U-2H3
120 mMDMPC[U-2H]3
200 mMDHPC[U-2H]3
10 mMMESnatural abundance3
100 mMsodium chloridenatural abundance3
0.4 mMBax a_2_a_5U-98% 13C6
120 mMDMPC[U-2H]6
200 mMDHPC[U-2H]6
10 mMMESnatural abundance6
100 mMsodium chloridenatural abundance6
0.6 mMBax a_2_a_5U-98% 15N;U-2H4
100 mMDMPCnatural abundance4
160 mMDHPC[U-2H]4
10 mMMESnatural abundance4
100 mMsodium chloridenatural abundance4
0.4 mMBax a_2_a_5U-98% 15N;U-15% 13C5
80 mMDMPCnatural abundance5
140 mMDHPCnatural abundance5
10 mMMESnatural abundance5
100 mMsodium chloridenatural abundance5
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002
Agilent DD2AgilentDD28003

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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 Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
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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