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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 / 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 / response to salt stress / release of sequestered calcium ion into cytosol / 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)
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: Zhang Y / Tian L / Huang G / Ge X / Kong F / Wang P / Xu Y / Shi Y
History
DepositionJul 29, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 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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