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- PDB-6el1: YaxAB pore complex -

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Basic information

Entry
Database: PDB / ID: 6el1
TitleYaxAB pore complex
Components
  • YaxA
  • YaxB
KeywordsMEMBRANE PROTEIN / Pore-forming toxin / Pathogens / Two-component toxin
Function / homology: / membrane => GO:0016020 / Uncharacterized protein / Putative membrane protein / Alpha-xenorhabdolysin family binary toxin subunit B
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsBraeuning, B. / Bertosin, E. / Dietz, H. / 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 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • EMDB-3885
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: YaxA
O: YaxB
A: YaxA
K: YaxB
B: YaxA
L: YaxB
C: YaxA
M: YaxB
D: YaxA
N: YaxB
F: YaxA
P: YaxB
G: YaxA
Q: YaxB
H: YaxA
R: YaxB
I: YaxA
S: YaxB
J: YaxA
T: YaxB


Theoretical massNumber of molelcules
Total (without water)851,26020
Polymers851,26020
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area78330 Å2
ΔGint-167 kcal/mol
Surface area347530 Å2
MethodPISA

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Components

#1: Protein
YaxA


Mass: 45877.156 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: ERS137951_00706 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T9S5R5, UniProt: A1JM51*PLUS
#2: Protein
YaxB


Mass: 39248.836 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: YE1985 / Production host: Escherichia coli (E. coli) / References: UniProt: A1JM52

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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

ComponentName: YaxAB complex (10x YaxA + 10x YaxB) / Type: COMPLEX
Details: Purified with Cymal-6 detergent and reconstituted in amphipol prior to Cryo-EM.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.85 MDa / Experimental value: YES
Source (natural)Organism: Yersinia enterocolitica (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESHEPES1
2100 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample exchanged to amphibole A8-35 and run in final round of gel filtration (buffer: 20 mM HEPES pH 7.0, 100 mM NaCl) prior to Cryo-EM.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 20 K
Details: 3 mM F-FOS Choline 8 just before vitrification blot for 3 to 4 s blot distance -2 to -1 mm

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION2.1particle selection
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinementphenix.real_space_refine
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 178000
SymmetryPoint symmetry: C10 (10 fold cyclic)
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25000 / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1OTHERREAL
2
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16EK7

6ek7

16EK71PDBexperimental model
16EK8

6ek8

26EK82PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00555050
ELECTRON MICROSCOPYf_angle_d0.93474080
ELECTRON MICROSCOPYf_dihedral_angle_d6.92334430
ELECTRON MICROSCOPYf_chiral_restr0.0498860
ELECTRON MICROSCOPYf_plane_restr0.0069410

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