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- EMDB-3885: YaxAB pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3885
TitleYaxAB pore complex
Map data
Sample
  • Complex: YaxAB complex (10x YaxA + 10x YaxB)
    • Protein or peptide: YaxA
    • Protein or peptide: YaxB
KeywordsPore-forming toxin / Pathogens / Two-component toxin / MEMBRANE PROTEIN
Function / homology: / membrane => GO:0016020 / membrane / Uncharacterized protein / Membrane protein / Alpha-xenorhabdolysin family binary toxin subunit B
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
Methodsingle 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, 2017-
Header (metadata) releaseOct 4, 2017-
Map releaseMay 16, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6el1
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3885.png

Downloads & links

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Map

FileDownload / File: emd_3885.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 400 pix.
= 442.4 Å		1.11 Å/pix.
x 400 pix.
= 442.4 Å		1.11 Å/pix.
x 400 pix.
= 442.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.106 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.02732106 - 0.14460759
Average (Standard dev.)0.00082460826 (±0.0069432124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 442.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1061.1061.106
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z442.400442.400442.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0270.1450.001

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Supplemental data

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Half map: #1

Fileemd_3885_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_3885_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : YaxAB complex (10x YaxA + 10x YaxB)

EntireName: YaxAB complex (10x YaxA + 10x YaxB)
Components
  • Complex: YaxAB complex (10x YaxA + 10x YaxB)
    • Protein or peptide: YaxA
    • Protein or peptide: YaxB

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Supramolecule #1: YaxAB complex (10x YaxA + 10x YaxB)

SupramoleculeName: YaxAB complex (10x YaxA + 10x YaxB) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Purified with Cymal-6 detergent and reconstituted in amphipol prior to Cryo-EM.
Source (natural)Organism: Yersinia enterocolitica (bacteria)
Molecular weightTheoretical: 850 KDa

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Macromolecule #1: YaxA

MacromoleculeName: YaxA / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Yersinia enterocolitica (bacteria)
Molecular weightTheoretical: 45.877156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TQTQLAIDNV LASAESTIQL NELPKVVLDF ITGEQTSVAR SGGIFTKEDL INLKLYVRKG LSLPTRQDEV EAYLGYKKID VAGLEPKDI KLLFDEIHNH ALNWNDVEQA VLQQSLDLDI AAKNIISTGN EIINLINQMP ITLRVKTLLG DITDKQLENI T YESADHEV ...String:
TQTQLAIDNV LASAESTIQL NELPKVVLDF ITGEQTSVAR SGGIFTKEDL INLKLYVRKG LSLPTRQDEV EAYLGYKKID VAGLEPKDI KLLFDEIHNH ALNWNDVEQA VLQQSLDLDI AAKNIISTGN EIINLINQMP ITLRVKTLLG DITDKQLENI T YESADHEV ASALKDILDD MKGDINRHQT TTENVRKKVS DYRITLTGGE LSSGDKVNGL EPQVKTKYDL MEKSNMRKSI KE LDEKIKE KRQRIEQLKK DYDKFVGLSF TGAIGGIIAM AITGGIFGAK AENARKEKNA LISEVAELES KVSSQRALQT ALE ALSLSF SDIGIRMVDA ESALNHLDFM WLSVLNQITE SQIQFAMINN ALRLTSFVNK FQQVITPWQS VGDSARQLVD IFDE AIKEY KKVYG

UniProtKB: Uncharacterized protein

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Macromolecule #2: YaxB

MacromoleculeName: YaxB / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Yersinia enterocolitica (bacteria)
Molecular weightTheoretical: 39.248836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAEISTFPHS GLSYPDINFK IFSQGVKNIS HLAQFKTTGV EVLQEKALRV SLYSQRLDVI VRESLSSLQV KLENTLALTY FTTLEEIDE ALISQDIDEE SKSEMRKERI NIIKNLSNDI TQLKQLFIEK TELLDKSSSD LHNVVIIEGT DKVLQAEQLR Q KQLTEDIA ...String:
GAEISTFPHS GLSYPDINFK IFSQGVKNIS HLAQFKTTGV EVLQEKALRV SLYSQRLDVI VRESLSSLQV KLENTLALTY FTTLEEIDE ALISQDIDEE SKSEMRKERI NIIKNLSNDI TQLKQLFIEK TELLDKSSSD LHNVVIIEGT DKVLQAEQLR Q KQLTEDIA TKELERKEIE KKRDKIIEAL DVIREHNLVD AFKDLIPTGE NLSELDLAKP EIELLKQSLE ITKKLLGQFS EG LKYIDLT DARKKLDNQI DTASTRLTEL NRQLEQSEKL IAGVNAVIKI DQEKSAVVVE AEKLSRAWHI FIHEITALQG TSL NEVELS KPLIKQQIYL ESLIKQLI

UniProtKB: Alpha-xenorhabdolysin family binary toxin subunit B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClsodium chloride
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.004 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 20 K / Instrument: FEI VITROBOT MARK IV
Details: 3 mM F-FOS Choline 8 just before vitrification blot for 3 to 4 s blot distance -2 to -1 mm.
DetailsSample 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.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 178000
Startup modelType of model: OTHER / Details: negative-stain reconstruction of the same sample
Final reconstructionApplied symmetry - Point group: C10 (10 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 25000
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
Final 3D classificationNumber classes: 7 / Avg.num./class: 16000 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ek7


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6el1:
YaxAB pore complex

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Atomic model buiding 2

Initial modelPDB ID:

6ek8


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6el1:
YaxAB pore complex

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