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- PDB-6gy6: XaxAB pore complex from Xenorhabdus nematophila -

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Basic information

Entry
Database: PDB / ID: 6gy6
TitleXaxAB pore complex from Xenorhabdus nematophila
Components
  • XaxA
  • XaxB
KeywordsTOXIN / bacterial toxin / pore forming-toxins
Function / homology: / membrane / XaxA / XaxB
Function and homology information
Biological speciesXenorhabdus nematophila ATCC 19061 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsSchubert, E. / Raunser, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Elife / Year: 2018
Title: Membrane insertion of α-xenorhabdolysin in near-atomic detail.
Authors: Evelyn Schubert / Ingrid R Vetter / Daniel Prumbaum / Pawel A Penczek / Stefan Raunser /
Abstract: α-Xenorhabdolysins (Xax) are α-pore-forming toxins (α-PFT) that form 1-1.3 MDa large pore complexes to perforate the host cell membrane. PFTs are used by a variety of bacterial pathogens to attack ...α-Xenorhabdolysins (Xax) are α-pore-forming toxins (α-PFT) that form 1-1.3 MDa large pore complexes to perforate the host cell membrane. PFTs are used by a variety of bacterial pathogens to attack host cells. Due to the lack of structural information, the molecular mechanism of action of Xax toxins is poorly understood. Here, we report the cryo-EM structure of the XaxAB pore complex from and the crystal structures of the soluble monomers of XaxA and XaxB. The structures reveal that XaxA and XaxB are built similarly and appear as heterodimers in the 12-15 subunits containing pore, classifying XaxAB as bi-component α-PFT. Major conformational changes in XaxB, including the swinging out of an amphipathic helix are responsible for membrane insertion. XaxA acts as an activator and stabilizer for XaxB that forms the actual transmembrane pore. Based on our results, we propose a novel structural model for the mechanism of Xax intoxication.
History
DepositionJun 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / em_entity_assembly_molwt / pdbx_entry_details
Item: _em_admin.last_update / _em_entity_assembly_molwt.id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: XaxA
B: XaxB
G: XaxB
H: XaxB
K: XaxB
L: XaxB
N: XaxB
O: XaxB
U: XaxB
V: XaxB
W: XaxB
X: XaxB
Y: XaxB
Z: XaxB
C: XaxA
D: XaxA
E: XaxA
F: XaxA
I: XaxA
J: XaxA
M: XaxA
P: XaxA
Q: XaxA
R: XaxA
S: XaxA
T: XaxA


Theoretical massNumber of molelcules
Total (without water)1,117,79926
Polymers1,117,79926
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area126610 Å2
ΔGint-366 kcal/mol
Surface area415220 Å2
MethodPISA

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Components

#1: Protein
XaxA


Mass: 47465.859 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus nematophila ATCC 19061 (bacteria)
Gene: xaxA, XNC1_3766 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): RIPL / References: UniProt: D3VB22
#2: Protein
XaxB


Mass: 38518.688 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus nematophila ATCC 19061 (bacteria)
Gene: xaxB, XNC1_3767 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): RIPL / References: UniProt: D3VB23
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1XaxAB complex (13 XaxA + 13 XaxB)COMPLEXall0RECOMBINANT
2XaxA protomerCOMPLEX#11RECOMBINANT13 XaxA protomers in the XaxAB pore complex
3XaxB protomerCOMPLEX#21RECOMBINANT13 XaxB protomers in the XaxAB pore complex
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.144 MDaNO
21NO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Xenorhabdus nematophila ATCC 19061 (bacteria)406817
32Xenorhabdus nematophila ATCC 19061 (bacteria)406817
43Xenorhabdus nematophila ATCC 19061 (bacteria)406817
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli BL21 (bacteria)511693RIPL
32Escherichia coli BL21 (bacteria)511693RIPL
43Escherichia coli BL21 (bacteria)511693RIPL
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/1
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategoryDetails
9SPHIREinitial Euler assignmentRVIPER
10SPHIREfinal Euler assignmentMERIDIEN
11SPHIREclassificationISAC
12SPHIRE3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C13 (13 fold cyclic)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43305 / Symmetry type: POINT

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