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- PDB-9ixu: Overall reconstruction of the Bax line -

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Basic information

Entry
Database: PDB / ID: 9ixu
TitleOverall reconstruction of the Bax line
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / Pore forming Bax proteins
Function / homology
Function and homology information


positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / development of animal secondary sexual characteristics / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / regulation of mammary gland epithelial cell proliferation ...positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / development of animal secondary sexual characteristics / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / spermatid differentiation / Sertoli cell proliferation / NTRK3 as a dependence receptor / positive regulation of apoptotic DNA fragmentation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell homeostatic proliferation / apoptotic process involved in mammary gland involution / apoptotic process involved in embryonic digit morphogenesis / B cell negative selection / BAK complex / retinal cell programmed cell death / glycosphingolipid metabolic process / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of apoptotic process involved in mammary gland involution / B cell apoptotic process / regulation of nitrogen utilization / endoplasmic reticulum calcium ion homeostasis / fertilization / epithelial cell apoptotic process / motor neuron apoptotic process / calcium ion transport into cytosol / positive regulation of epithelial cell apoptotic process / mitochondrial fusion / myeloid cell homeostasis / Bcl-2 family protein complex / execution phase of apoptosis / odontogenesis of dentin-containing tooth / thymocyte apoptotic process / B cell homeostasis / hypothalamus development / positive regulation of IRE1-mediated unfolded protein response / pore complex / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / vagina development / germ cell development / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / negative regulation of apoptotic signaling pathway / cellular response to unfolded protein / positive regulation of calcium ion transport into cytosol / Pyroptosis / response to axon injury / blood vessel remodeling / negative regulation of protein binding / ectopic germ cell programmed cell death / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / ovarian follicle development / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / release of sequestered calcium ion into cytosol / positive regulation of intrinsic apoptotic signaling pathway / response to salt stress / supramolecular fiber organization / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / intrinsic apoptotic signaling pathway / Hsp70 protein binding / positive regulation of release of sequestered calcium ion into cytosol / regulation of mitochondrial membrane potential / kidney development / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / cerebral cortex development / cellular response to virus / neuron migration / intrinsic apoptotic signaling pathway in response to DNA damage / response to toxic substance / cellular response to UV / nuclear envelope / positive regulation of neuron apoptotic process / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsZhang, Y. / Tian, L. / Ge, X. / Huang, G. / Shi, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509300 China
National Natural Science Foundation of China (NSFC)81920108015 China
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Science / Year: 2025
Title: Structural basis of BAX pore formation.
Authors: Ying Zhang / Lu Tian / Gaoxingyu Huang / Xiaofei Ge / Fang Kong / Pengqi Wang / Yige Xu / Yigong Shi /
Abstract: During apoptosis, cytosolic BAX monomers are translocated to the mitochondria to permeabilize the outer membrane. Here, we identified a dimer of BAX dimers as the basic repeating unit of its various ...During apoptosis, cytosolic BAX monomers are translocated to the mitochondria to permeabilize the outer membrane. Here, we identified a dimer of BAX dimers as the basic repeating unit of its various oligomeric forms: arcs, lines, and rings. Cryo-electron microscopy structure of the BAX repeating unit at 3.2-angstrom resolution revealed the interactions within and between dimers. End-to-end stacking of the repeating units through the protruding α9 pairs yielded lines, arcs, polygons, and rings. We structurally characterized the tetragon, pentagon, hexagon, and heptagon, which comprise 16, 20, 24, and 28 BAX protomers, respectively. Missense mutations at the BAX inter-protomer interface damage pore formation and cripple its proapoptotic function. The assembly principle of the various BAX oligomers reported here provides the structural basis of membrane permeabilization by BAX.
History
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Dec 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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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
E: Apoptosis regulator BAX
F: Apoptosis regulator BAX
C: Apoptosis regulator BAX
D: Apoptosis regulator BAX
G: Apoptosis regulator BAX
H: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)169,6358
Polymers169,6358
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 21204.355 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Homo sapiens (human) / References: UniProt: Q07812
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bax line / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 18000 nm / Nominal defocus min: 13000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.17.1_3660: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190916 / Symmetry type: POINT

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