+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3885 | |||||||||
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Title | YaxAB pore complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Pore-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 species | Yersinia enterocolitica (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
Authors | Braeuning B / Bertosin E / Dietz H / Groll M | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3885.map.gz | 21.4 MB | EMDB map data format | |
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Header (meta data) | emd-3885-v30.xml emd-3885.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3885_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_3885.png | 28.7 KB | ||
Filedesc metadata | emd-3885.cif.gz | 6.2 KB | ||
Others | emd_3885_half_map_1.map.gz emd_3885_half_map_2.map.gz | 192 MB 192.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3885 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3885 | HTTPS FTP |
-Validation report
Summary document | emd_3885_validation.pdf.gz | 344.6 KB | Display | EMDB validaton report |
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Full document | emd_3885_full_validation.pdf.gz | 343.7 KB | Display | |
Data in XML | emd_3885_validation.xml.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3885 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3885 | HTTPS FTP |
-Related structure data
Related structure data | 6el1MC 6ek4C 6ek7C 6ek8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3885.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.106 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_3885_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_3885_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : YaxAB complex (10x YaxA + 10x YaxB)
Entire | Name: YaxAB complex (10x YaxA + 10x YaxB) |
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Components |
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-Supramolecule #1: YaxAB complex (10x YaxA + 10x YaxB)
Supramolecule | Name: 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. |
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Source (natural) | Organism: Yersinia enterocolitica (bacteria) |
Molecular weight | Theoretical: 850 KDa |
-Macromolecule #1: YaxA
Macromolecule | Name: YaxA / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Yersinia enterocolitica (bacteria) |
Molecular weight | Theoretical: 45.877156 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: YaxB
Macromolecule | Name: YaxB / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Yersinia enterocolitica (bacteria) |
Molecular weight | Theoretical: 39.248836 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||
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Buffer | pH: 7 Component:
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Grid | Model: 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 | |||||||||
Vitrification | Cryogen 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. | |||||||||
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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-6el1: |