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- PDB-6gy8: Crystal structure of XaxA from Xenorhabdus nematophila -

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Basic information

Entry
Database: PDB / ID: 6gy8
TitleCrystal structure of XaxA from Xenorhabdus nematophila
ComponentsXaxA
KeywordsTOXIN / bacterial toxin / pore forming-toxins
Function / homologyHemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Up-down Bundle / Mainly Alpha / membrane / XaxA
Function and homology information
Biological speciesXenorhabdus nematophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XaxA
B: XaxA


Theoretical massNumber of molelcules
Total (without water)91,1902
Polymers91,1902
Non-polymers00
Water4,396244
1
A: XaxA


Theoretical massNumber of molelcules
Total (without water)45,5951
Polymers45,5951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: XaxA


Theoretical massNumber of molelcules
Total (without water)45,5951
Polymers45,5951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.270, 90.830, 153.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein XaxA


Mass: 45594.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6) (bacteria)
Gene: xaxA, XNC1_3766 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): RIPL / References: UniProt: D3VB22
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M sodium chloride, 0.1 M phosphate citrate pH 4.2, 10 % PEG 3000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, DESY P1111.8233
SYNCHROTRONSLS X06DA22
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELNov 6, 2016
DECTRIS EIGER X 16M2PIXELNov 26, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.82331
221
ReflectionResolution: 2.5→50 Å / Num. obs: 62589 / % possible obs: 99.9 % / Redundancy: 15.93 % / Net I/σ(I): 18.47
Reflection shellResolution: 2.5→2.56 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.415 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.27
RfactorNum. reflection% reflection
Rfree0.2856 3124 4.99 %
Rwork0.2382 --
obs0.2406 62573 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 0 0 244 5616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025435
X-RAY DIFFRACTIONf_angle_d0.4627304
X-RAY DIFFRACTIONf_dihedral_angle_d10.0623378
X-RAY DIFFRACTIONf_chiral_restr0.035850
X-RAY DIFFRACTIONf_plane_restr0.003933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53910.40541540.35132669X-RAY DIFFRACTION100
2.5391-2.58070.47171490.35652733X-RAY DIFFRACTION100
2.5807-2.62520.42071320.34562695X-RAY DIFFRACTION100
2.6252-2.6730.37331370.33572681X-RAY DIFFRACTION100
2.673-2.72440.40051290.31822702X-RAY DIFFRACTION100
2.7244-2.780.42721410.31952725X-RAY DIFFRACTION100
2.78-2.84040.31951420.30122731X-RAY DIFFRACTION100
2.8404-2.90650.40651410.30612683X-RAY DIFFRACTION100
2.9065-2.97910.43221430.33152692X-RAY DIFFRACTION100
2.9791-3.05970.36651440.32232734X-RAY DIFFRACTION100
3.0597-3.14970.38971410.30852676X-RAY DIFFRACTION100
3.1497-3.25130.35671450.28792706X-RAY DIFFRACTION100
3.2513-3.36750.29161400.27092702X-RAY DIFFRACTION100
3.3675-3.50230.36851350.25512698X-RAY DIFFRACTION100
3.5023-3.66160.26091450.24882712X-RAY DIFFRACTION100
3.6616-3.85450.33531450.23612675X-RAY DIFFRACTION100
3.8545-4.09590.24351420.21712696X-RAY DIFFRACTION100
4.0959-4.41190.2581430.18972724X-RAY DIFFRACTION100
4.4119-4.85540.22371470.19422704X-RAY DIFFRACTION100
4.8554-5.5570.21961410.21952711X-RAY DIFFRACTION100
5.557-6.99710.27511440.23582699X-RAY DIFFRACTION100
6.9971-45.42250.19441440.16612701X-RAY DIFFRACTION100

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