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- EMDB-9011: Bax with activating Bid peptide inserted into nanodisc. -

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Basic information

Entry
Database: EMDB / ID: EMD-9011
TitleBax with activating Bid peptide inserted into nanodisc.
Map dataBax with activating Bid peptide inserted in nanodiscs
Sample
  • Complex: Complex of Bax and activating Bid peptide inserted in nanodisc
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 28.0 Å
AuthorsVolkmann N / Hanein D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer InstituteR01 CA179087 United States
CitationJournal: Structure / Year: 2019
Title: Biophysical Characterization of a Nanodisc with and without BAX: An Integrative Study Using Molecular Dynamics Simulations and Cryo-EM.
Authors: Cesar A López / Mark F Swift / Xiao-Ping Xu / Dorit Hanein / Niels Volkmann / S Gnanakaran /
Abstract: B cell lymphoma-2-associated X protein (BAX) plays a pivotal role in triggering cell apoptosis by permeabilizing the mitochondrial outer membrane. Contrary to previous findings, recent electron ...B cell lymphoma-2-associated X protein (BAX) plays a pivotal role in triggering cell apoptosis by permeabilizing the mitochondrial outer membrane. Contrary to previous findings, recent electron microscopy (EM) experiments showed that BAX monomers are able to perturb phospholipid nanodiscs (NDs) by forming lipidic pores. Here, we provide structural and thermodynamic interpretation of such data using multiscale resolution molecular dynamics (MD) simulations. Our results suggest that BAX is able to disrupt the stability, lateral packing and enhance the desorption propensity of the lipids in the ND, resulting in the formation of a stable toroidal-like pore. These findings prompted to re-evaluate the previously reported cryo-EM data to generate an improved reconstruction, thereby allowing for a more accurate localization of BAX in the EM map. We conclude that the reduced stability of the BAX-embedded ND eliminates the necessity of forming active BAX oligomers for its disruption.
History
DepositionJul 31, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseAug 28, 2019-
UpdateAug 28, 2019-
Current statusAug 28, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9011.png

Downloads & links

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Map

FileDownload / File: emd_9011.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBax with activating Bid peptide inserted in nanodiscs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.76 Å/pix.
x 40 pix.
= 270.4 Å		6.76 Å/pix.
x 40 pix.
= 270.4 Å		6.76 Å/pix.
x 40 pix.
= 270.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-2.7863584 - 14.228982999999999
Average (Standard dev.)0.000000005588786 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions404040
Spacing404040
CellA=B=C: 270.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.766.766.76
M x/y/z404040
origin x/y/z0.0000.0000.000
length x/y/z270.400270.400270.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ132132232
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404040
D min/max/mean-2.78614.2290.000

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Supplemental data

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Sample components

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Entire : Complex of Bax and activating Bid peptide inserted in nanodisc

EntireName: Complex of Bax and activating Bid peptide inserted in nanodisc
Components
  • Complex: Complex of Bax and activating Bid peptide inserted in nanodisc

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Supramolecule #1: Complex of Bax and activating Bid peptide inserted in nanodisc

SupramoleculeName: Complex of Bax and activating Bid peptide inserted in nanodisc
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: KODAK SO-163 FILM / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: EMAN2
Startup modelType of model: OTHER
Details: Previously obtained reconstructions of the same sample
Final reconstructionResolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4312
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2

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