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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


release of matrix enzymes from mitochondria / BAX complex / B cell receptor apoptotic signaling pathway / Activation, translocation and oligomerization of BAX / B cell apoptotic process / positive regulation of apoptotic DNA fragmentation / NTRK3 as a dependence receptor / BAK complex / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process ...release of matrix enzymes from mitochondria / BAX complex / B cell receptor apoptotic signaling pathway / Activation, translocation and oligomerization of BAX / B cell apoptotic process / positive regulation of apoptotic DNA fragmentation / NTRK3 as a dependence receptor / BAK complex / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process / Release of apoptotic factors from the mitochondria / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / endoplasmic reticulum calcium ion homeostasis / mitochondrial fusion / apoptotic mitochondrial changes / execution phase of apoptosis / Bcl-2 family protein complex / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of IRE1-mediated unfolded protein response / pore complex / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / cellular response to unfolded protein / Pyroptosis / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein binding / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Hsp70 protein binding / regulation of mitochondrial membrane potential / apoptotic signaling pathway / cellular response to virus / positive regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage / response to toxic substance / positive regulation of neuron apoptotic process / nuclear envelope / channel activity / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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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