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- PDB-6ek4: PaxB from Photorhabdus luminescens -

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Basic information

Entry
Database: PDB / ID: 6ek4
TitlePaxB from Photorhabdus luminescens
ComponentsPaxB
KeywordsMEMBRANE PROTEIN / pathogens / pore forming toxins / alpha-helical / adventitious membrane protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PaxB
B: PaxB
C: PaxB
D: PaxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,7988
Polymers162,7064
Non-polymers924
Water4,071226
1
A: PaxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7233
Polymers40,6771
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PaxB


Theoretical massNumber of molelcules
Total (without water)40,6771
Polymers40,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PaxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7002
Polymers40,6771
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PaxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7002
Polymers40,6771
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.590, 70.180, 136.890
Angle α, β, γ (deg.)90.00, 108.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PaxB


Mass: 40676.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: Phpb_01513 / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B8YJW8*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M MgCl2; 0.1 M Bis-Tris, 25% PEG 3350; 0.2M NaSCN

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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: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 44675 / % possible obs: 95.3 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rrim(I) all: 0.069 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.8 / CC1/2: 0.729 / Rrim(I) all: 0.515 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Semet derivative of PaxB

Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 34.529 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26835 2234 5 %RANDOM
Rwork0.2405 ---
obs0.24205 42429 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.879 Å2
Baniso -1Baniso -2Baniso -3
1--3.67 Å2-0 Å20.04 Å2
2---2.37 Å20 Å2
3---4.93 Å2
Refinement stepCycle: 1 / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10648 0 4 226 10878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01910738
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210991
X-RAY DIFFRACTIONr_angle_refined_deg0.6961.98414439
X-RAY DIFFRACTIONr_angle_other_deg0.646325292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.99251309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62125.863527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.744152255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7611574
X-RAY DIFFRACTIONr_chiral_restr0.0410.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022232
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_it0.8346.5365260
X-RAY DIFFRACTIONr_mcbond_other0.8346.5365259
X-RAY DIFFRACTIONr_mcangle_it1.5279.7966561
X-RAY DIFFRACTIONr_mcangle_other1.5279.7966562
X-RAY DIFFRACTIONr_scbond_it0.6076.6495478
X-RAY DIFFRACTIONr_scbond_other0.6076.6485477
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1629.9427878
X-RAY DIFFRACTIONr_long_range_B_refined3.60149.91712385
X-RAY DIFFRACTIONr_long_range_B_other3.55449.89212366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 155 -
Rwork0.363 2938 -
obs--93.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0464-1.77990.6361.1317-0.40080.1462-0.0671-0.2102-0.21730.06530.11840.162-0.0096-0.0252-0.05140.14870.12370.05250.21890.17050.205-18.5229-33.5777-24.8693
22.0692-2.39781.51232.9464-1.80441.16710.04730.04590.1741-0.1068-0.2067-0.2937-0.01640.11240.15940.13860.04020.01360.23130.10270.18190.7341-6.5901-37.4063
32.1946-1.53861.36811.4249-1.13541.0018-0.1013-0.24240.06130.20630.0533-0.0238-0.2069-0.05720.0480.30.0920.00510.27340.0020.0111-19.56833.9257-24.2549
42.2605-2.06880.29572.1243-0.38640.11060.14990.0456-0.1013-0.1786-0.07710.11260.04030.006-0.07280.19010.1115-0.02720.19930.01590.1567-27.7013-18.978-48.8056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 353
2X-RAY DIFFRACTION2B11 - 353
3X-RAY DIFFRACTION3C12 - 353
4X-RAY DIFFRACTION4D12 - 353

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