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- EMDB-60977: Overall reconstruction of the Bax line -

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Basic information

Entry
Database: EMDB / ID: EMD-60977
TitleOverall reconstruction of the Bax line
Map dataC2 symmetrized composite map of the Bax line sample.
Sample
  • Complex: Bax line
    • Protein or peptide: Apoptosis regulator BAX
KeywordsPore forming Bax proteins / APOPTOSIS
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 / Activation, translocation and oligomerization of BAX ...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 / Activation, translocation and oligomerization of BAX / spermatid differentiation / Sertoli cell proliferation / NTRK3 as a dependence receptor / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / positive regulation of B cell apoptotic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell homeostatic proliferation / glycosphingolipid metabolic process / B cell negative selection / BAK complex / 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 / mitochondrial fragmentation involved in apoptotic process / apoptotic process involved in blood vessel morphogenesis / 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 / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of epithelial cell apoptotic process / fertilization / calcium ion transport into cytosol / epithelial cell apoptotic process / mitochondrial fusion / myeloid cell homeostasis / Bcl-2 family protein complex / motor neuron apoptotic process / execution phase of apoptosis / thymocyte apoptotic process / pore complex / hypothalamus development / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / BH3 domain binding / vagina development / B cell homeostasis / negative regulation of mitochondrial membrane potential / positive regulation of calcium ion transport into cytosol / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / ectopic germ cell programmed cell death / response to axon injury / negative regulation of fibroblast proliferation / negative regulation of protein binding / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / extrinsic apoptotic signaling pathway / response to salt stress / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / Hsp70 protein binding / regulation of mitochondrial membrane potential / homeostasis of number of cells within a tissue / 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 / response to gamma radiation / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / kidney development / cerebral cortex development / cellular response to virus / response to toxic substance / neuron migration / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / nuclear envelope / positive regulation of neuron apoptotic process / retina development in camera-type eye / channel activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsZhang Y / Tian L / Ge X / Huang G / Shi Y
Funding support China, 3 items
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, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60977.png

Downloads & links

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Map

FileDownload / File: emd_60977.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC2 symmetrized composite map of the Bax line sample.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.54
Minimum - Maximum-0.121681504 - 17.841919000000001
Average (Standard dev.)-0.05611281 (±0.40500247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60977_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C1 reconstruction of the Bax line sample.

Fileemd_60977_additional_1.map
AnnotationC1 reconstruction of the Bax line sample.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A map of the C1 reconstruction of the Bax line sample.

Fileemd_60977_half_map_1.map
Annotationhalf A map of the C1 reconstruction of the Bax line sample.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map of the C1 reconstruction of the Bax line sample

Fileemd_60977_half_map_2.map
Annotationhalf B map of the C1 reconstruction of the Bax line sample
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bax line

EntireName: Bax line
Components
  • Complex: Bax line
    • Protein or peptide: Apoptosis regulator BAX

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Supramolecule #1: Bax line

SupramoleculeName: Bax line / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Apoptosis regulator BAX

MacromoleculeName: Apoptosis regulator BAX / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.204355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDGSGEQPRG GGPTSSEQIM KTGALLLQGF IQDRAGRMGG EAPELALDPV PQDASTKKLS ECLKRIGDEL DSNMELQRMI AAVDTDSPR EVFFRVAADM FSDGNFNWGR VVALFYFASK LVLKALCTKV PELIRTIMGW TLDFLRERLL GWIQDQGGWD G LLSYFGTP ...String:
MDGSGEQPRG GGPTSSEQIM KTGALLLQGF IQDRAGRMGG EAPELALDPV PQDASTKKLS ECLKRIGDEL DSNMELQRMI AAVDTDSPR EVFFRVAADM FSDGNFNWGR VVALFYFASK LVLKALCTKV PELIRTIMGW TLDFLRERLL GWIQDQGGWD G LLSYFGTP TWQTVTIFVA GVLTASLTIW KKMG

UniProtKB: Apoptosis regulator BAX

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 18.0 µm / Nominal defocus min: 13.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 190916
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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