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- EMDB-13185: Helical structure of the toxin MakA from Vibrio cholera -

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Basic information

Entry
Database: EMDB / ID: EMD-13185
TitleHelical structure of the toxin MakA from Vibrio cholera
Map data
Sample
  • Complex: Vibrio cholera MakA filament
    • Protein or peptide: MakA tetramer
KeywordsPore-forming toxin / Vibrio cholerae / TOXIN
Function / homologyHemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / : / membrane / Non-hemolytic enterotoxin lytic component L1
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria) / Vibrio cholerae O1 biovar El Tor str. N16961
Methodhelical reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsBerg A / Nadeem A
Funding support Sweden, European Union, 4 items
OrganizationGrant numberCountry
Swedish Research Council2019-02011 Sweden
European Research Council (ERC)948655European Union
Swedish Research Council2018-02914 Sweden
Swedish Research Council2019-01720 Sweden
CitationJournal: Elife / Year: 2022
Title: Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from .
Authors: Aftab Nadeem / Alexandra Berg / Hudson Pace / Athar Alam / Eric Toh / Jörgen Ådén / Nikola Zlatkov / Si Lhyam Myint / Karina Persson / Gerhard Gröbner / Anders Sjöstedt / Marta Bally / ...Authors: Aftab Nadeem / Alexandra Berg / Hudson Pace / Athar Alam / Eric Toh / Jörgen Ådén / Nikola Zlatkov / Si Lhyam Myint / Karina Persson / Gerhard Gröbner / Anders Sjöstedt / Marta Bally / Jonas Barandun / Bernt Eric Uhlin / Sun Nyunt Wai /
Abstract: The α-pore-forming toxins (α-PFTs) from pathogenic bacteria damage host cell membranes by pore formation. We demonstrate a remarkable, hitherto unknown mechanism by an α-PFT protein from . As part ...The α-pore-forming toxins (α-PFTs) from pathogenic bacteria damage host cell membranes by pore formation. We demonstrate a remarkable, hitherto unknown mechanism by an α-PFT protein from . As part of the MakA/B/E tripartite toxin, MakA is involved in membrane pore formation similar to other α-PFTs. In contrast, MakA in isolation induces tube-like structures in acidic endosomal compartments of epithelial cells in vitro. The present study unravels the dynamics of tubular growth, which occurs in a pH-, lipid-, and concentration-dependent manner. Within acidified organelle lumens or when incubated with cells in acidic media, MakA forms oligomers and remodels membranes into high-curvature tubes leading to loss of membrane integrity. A 3.7 Å cryo-electron microscopy structure of MakA filaments reveals a unique protein-lipid superstructure. MakA forms a pinecone-like spiral with a central cavity and a thin annular lipid bilayer embedded between the MakA transmembrane helices in its active α-PFT conformation. Our study provides insights into a novel tubulation mechanism of an α-PFT protein and a new mode of action by a secreted bacterial toxin.
History
DepositionJul 8, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p3r
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7p3r
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13185.png

Downloads & links

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Map

FileDownload / File: emd_13185.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 460 pix.
= 479.32 Å		1.04 Å/pix.
x 460 pix.
= 479.32 Å		1.04 Å/pix.
x 460 pix.
= 479.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.042 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.014
Minimum - Maximum-0.052981388 - 0.09457739
Average (Standard dev.)0.0002856373 (±0.0043610274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 479.32004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0421.0421.042
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z479.320479.320479.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.0530.0950.000

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Supplemental data

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Additional map: additional map 1

Fileemd_13185_additional_1.map
Annotationadditional map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hafl map 2

Fileemd_13185_half_map_1.map
Annotationhafl map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: hafl map 1

Fileemd_13185_half_map_2.map
Annotationhafl map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vibrio cholera MakA filament

EntireName: Vibrio cholera MakA filament
Components
  • Complex: Vibrio cholera MakA filament
    • Protein or peptide: MakA tetramer

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Supramolecule #1: Vibrio cholera MakA filament

SupramoleculeName: Vibrio cholera MakA filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

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Macromolecule #1: MakA tetramer

MacromoleculeName: MakA tetramer / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961
Molecular weightTheoretical: 39.028582 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSQQVTQLNP TQQTTQSAFL ATTVITAQCH AILNTQFTPP TVKPDWFDDL SKKLDSAKLV AKQWIDDLGP QVSASIPSSV INFDATFQA SIDAIHELYK ADPTASGKDN TTVQQASQIM TALSSQVSGI EATVKGMNKE LSDWGVKMQA AHDDLVNGAT N IQKTIIDL ...String:
MSQQVTQLNP TQQTTQSAFL ATTVITAQCH AILNTQFTPP TVKPDWFDDL SKKLDSAKLV AKQWIDDLGP QVSASIPSSV INFDATFQA SIDAIHELYK ADPTASGKDN TTVQQASQIM TALSSQVSGI EATVKGMNKE LSDWGVKMQA AHDDLVNGAT N IQKTIIDL QTDIESMNNA IDNNRAAIEK LNKDLVYAQV AVGVGIFMLV AGVALTVATA GTAAAVSGGI AAVGAASIIA GG VTWGVLQ NQIDDDYDSI AQEQKQKAED QQQIIALQGL SNASSAVVSA IETSTSVLSD FETTWTVFGN ELDDVVTKLN NGA SMQSII MEKVMSDAAK NEWDDAVELA KQLASAKIAI ETKELAPAVK QAA

UniProtKB: Non-hemolytic enterotoxin lytic component L1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.5 / Component - Concentration: 120.0 mM / Component - Name: Sodium Citrate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2476 / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.84149 Å
Applied symmetry - Helical parameters - Δ&Phi: 48.5901 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 65485
Segment selectionNumber selected: 95603 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: OTHER
Details: featureless cylinder, created using the helix toolbox in RELION-3.1
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ezv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7p3r:
Helical structure of the toxin MakA from Vibrio cholera

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