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- PDB-6ek8: YaxB from Yersinia enterocolitica -

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Basic information

Entry
Database: PDB / ID: 6ek8
TitleYaxB from Yersinia enterocolitica
ComponentsYaxB
KeywordsMEMBRANE PROTEIN / pathogens / pore forming toxins / alpha-helical / adventitious membrane protein
Function / homology: / Alpha-xenorhabdolysin family binary toxin subunit B
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBraeuning, B. / Groll, M.
CitationJournal: Nat Commun / Year: 2018
Title: Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB.
Authors: Bastian Bräuning / Eva Bertosin / Florian Praetorius / Christian Ihling / Alexandra Schatt / Agnes Adler / Klaus Richter / Andrea Sinz / Hendrik Dietz / Michael Groll /
Abstract: Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, ...Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA-YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures.
History
DepositionSep 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: YaxB


Theoretical massNumber of molelcules
Total (without water)39,2491
Polymers39,2491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.700, 111.700, 169.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein YaxB


Mass: 39248.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: YE1985 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / References: UniProt: A1JM52

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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: 5.37 Å3/Da / Density % sol: 77.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.2 M Na/K-phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 5633 / % possible obs: 98.7 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13
Reflection shellResolution: 4→4.1 Å / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.73 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EK4

6ek4


Resolution: 4→48.82 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.928 / SU B: 155.607 / SU ML: 0.904 / Cross valid method: THROUGHOUT / ESU R Free: 0.847 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33881 282 5 %RANDOM
Rwork0.32555 ---
obs0.32625 5351 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 196.051 Å2
Baniso -1Baniso -2Baniso -3
1-6.23 Å23.11 Å20 Å2
2--6.23 Å20 Å2
3----20.2 Å2
Refinement stepCycle: 1 / Resolution: 4→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 0 0 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192016
X-RAY DIFFRACTIONr_bond_other_d0.0030.021995
X-RAY DIFFRACTIONr_angle_refined_deg0.9041.9842710
X-RAY DIFFRACTIONr_angle_other_deg0.99134646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6235245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93626.23793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34115424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5181510
X-RAY DIFFRACTIONr_chiral_restr0.0560.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022147
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02343
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.24816.217992
X-RAY DIFFRACTIONr_mcbond_other4.24916.218991
X-RAY DIFFRACTIONr_mcangle_it5.71424.3151233
X-RAY DIFFRACTIONr_mcangle_other5.71324.3131234
X-RAY DIFFRACTIONr_scbond_it3.98916.8071024
X-RAY DIFFRACTIONr_scbond_other3.98716.8041025
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.98725.0321478
X-RAY DIFFRACTIONr_long_range_B_refined8.3482458
X-RAY DIFFRACTIONr_long_range_B_other8.3472459
X-RAY DIFFRACTIONr_rigid_bond_restr1.7434011
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded78.00153997
LS refinement shellResolution: 4.001→4.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 20 -
Rwork0.408 377 -
obs--99.25 %
Refinement TLS params.Method: refined / Origin x: -15.9682 Å / Origin y: -43.3453 Å / Origin z: 12.9532 Å
111213212223313233
T0.2483 Å20.1377 Å2-0.0195 Å2-0.2365 Å2-0.0636 Å2--0.5704 Å2
L2.4129 °2-1.3972 °2-0.5031 °2-1.3647 °20.2915 °2--0.1944 °2
S0.0124 Å °-0.0748 Å °-0.488 Å °-0.1003 Å °-0.0419 Å °0.2381 Å °-0.1303 Å °-0.0028 Å °0.0295 Å °

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